* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Darwin.
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_wrapper.c -o R_wrapper.o
R_wrapper.c:32:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:58:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:85:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:111:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:136:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:160:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:187:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
R_wrapper.c:213:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
c_argv = (char **) calloc(n,sizeof(char *));
˜˜˜˜˜˜ ^
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c SNPCalling.c -o SNPCalling.o
SNPCalling.c:84:29: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
if(a*1./c < b*1./d) return 1.1;
˜˜˜˜˜˜ ^˜˜
SNPCalling.c:106:9: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return p_sum;
˜˜˜˜˜˜ ^˜˜˜˜
SNPCalling.c:158:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
first_base_pos = read_rec.pos - block_no * BASE_BLOCK_LENGTH;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:173:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char true_value = referenced_genome[i + first_base_pos -1];
^ ˜
SNPCalling.c:199:7: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(i+first_base_pos > reference_len || i+first_base_pos<1)
^˜
SNPCalling.c:199:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(i+first_base_pos > reference_len || i+first_base_pos<1)
^˜
SNPCalling.c:201:64: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
SUBREADprintf("Warning: read out of boundary: %u >= %u\n", i+first_base_pos, reference_len);
^˜
SNPCalling.c:220:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
supporting_bases += snp_voting_table_Neg[(first_base_pos+i-1)*4+j];
˜^
SNPCalling.c:220:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
supporting_bases += snp_voting_table_Neg[(first_base_pos+i-1)*4+j];
˜^
SNPCalling.c:221:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
supporting_bases += snp_voting_table_Pos[(first_base_pos+i-1)*4+j];
˜^
SNPCalling.c:221:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
supporting_bases += snp_voting_table_Pos[(first_base_pos+i-1)*4+j];
˜^
SNPCalling.c:226:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
snp_voting_table_Neg[(first_base_pos+i-1)*4+base_int]++;
˜^
SNPCalling.c:226:50: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
snp_voting_table_Neg[(first_base_pos+i-1)*4+base_int]++;
˜^˜˜˜˜˜˜˜
SNPCalling.c:228:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
snp_voting_table_Pos[(first_base_pos+i-1)*4+base_int]++;
˜^
SNPCalling.c:228:50: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
snp_voting_table_Pos[(first_base_pos+i-1)*4+base_int]++;
˜^˜˜˜˜˜˜˜
SNPCalling.c:310:47: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
c = snp_voting_table_Pos[ i * 4 + j ] + snp_voting_table_Neg[ i * 4 + j ];
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:151:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rret=fread(&read_rec, sizeof(read_rec), 1, tmp_fp);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:152:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rret=fread(&read_len, sizeof(short), 1, tmp_fp);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:153:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rret=fread(read, sizeof(char), read_len, tmp_fp);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:154:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
rret=fread(qual, sizeof(char), read_len, tmp_fp);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:437:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nc = fgetc(in_fp);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:445:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nc = toupper(nc);
˜ ^˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:419:36: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
chro_len = chromosomes[chro_no].known_length;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:630:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
while ((c = getopt (argc, argv, "N:I:p:q:i:o:r:t:g:n:c:m:?S")) != -1)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:694:41: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
parameters.neighbour_filter_rate = atof(optarg+t+1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:719:39: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
parameters.supporting_read_rate = atof(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:723:45: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
parameters.max_supporting_read_number = atof(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:727:45: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
parameters.min_supporting_read_number = atof(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:731:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
read_count = atoi(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
SNPCalling.c:682:7: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
k=strlen(optarg);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
30 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c aligner.c -o aligner.o
aligner.c:122:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
sprintf(nameb, "read_%llu", i+1+all_processed_reads);
˜^˜˜
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^
aligner.c:125:25: warning: implicit conversion changes signedness: 'gene_vote_number_t' (aka 'char') to 'unsigned char' [-Wsign-conversion]
unsigned char votes = av->max_votes[Curr_position];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:180:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int lpos = av->max_positions[Curr_position];
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:181:26: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
char is_counterpart = av->is_counterpart[Curr_position];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:210:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(!locate_gene_position_max(lpos, &offsets, &read_name, &read_pos, rl + rl_adj))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
aligner.c:229:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mate_pos += mate_offset_pos;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:234:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:234:66: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜˜
aligner.c:234:73: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:234:86: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜
aligner.c:234:98: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
aligner.c:234:124: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:234:142: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl1) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl2));
˜ ^˜˜
aligner.c:236:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:236:66: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜˜
aligner.c:236:73: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:236:86: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜
aligner.c:236:98: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜ ˜
aligner.c:236:124: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:236:142: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tlen = ( (mate_pos > lpos) ? (mate_pos - mate_offset_pos - lpos + offset_pos + rl2) :(lpos - offset_pos - mate_pos + mate_offset_pos + rl1));
˜ ^˜˜
aligner.c:334:51: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Saving results", i*1./processed_reads, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:421:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
queries = *processed_reads;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:448:53: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Finalising", queries*1./segment_length, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:502:66: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
find_and_explain_indel(allvote, queries*2 + read_second , pos_read , numvote_read , 0, r_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read_txt , rl , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_reverse, qual_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
aligner.c:502:77: warning: implicit conversion loses integer precision: 'int' to 'gene_vote_number_t' (aka 'char') [-Wconversion]
find_and_explain_indel(allvote, queries*2 + read_second , pos_read , numvote_read , 0, r_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read_txt , rl , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_reverse, qual_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
aligner.c:502:116: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
find_and_explain_indel(allvote, queries*2 + read_second , pos_read , numvote_read , 0, r_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read_txt , rl , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_reverse, qual_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:512:61: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
allvote->max_final_quality[queries*2 + read_second] = final_mapping_quality_edit(my_value_array_index, allvote->max_positions[queries *2 + read_second], read_txt, qual_txt, cigar_str, FASTQ_FORMAT, &mismatch, rl);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:513:57: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
allvote->edit_distance[queries*2 + read_second] = mismatch;
˜ ^˜˜˜˜˜˜˜
aligner.c:521:60: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
allvote->max_final_quality[queries*2 + read_second] = final_mapping_quality_edit(my_value_array_index, allvote->max_positions[queries *2 + read_second], read_txt, qual_txt, cigar_str, FASTQ_FORMAT, &mismatch, rl);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:522:56: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
allvote->edit_distance[queries*2 + read_second] = mismatch;
˜ ^˜˜˜˜˜˜˜
aligner.c:572:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
find_and_explain_indel(allvote, queries , pos_read , numvote_read , 0, r_need_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read1_txt , rl1 , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_need_reverse, qual1_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
aligner.c:572:60: warning: implicit conversion loses integer precision: 'int' to 'gene_vote_number_t' (aka 'char') [-Wconversion]
find_and_explain_indel(allvote, queries , pos_read , numvote_read , 0, r_need_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read1_txt , rl1 , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_need_reverse, qual1_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
aligner.c:572:104: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
find_and_explain_indel(allvote, queries , pos_read , numvote_read , 0, r_need_reverse , read_mask|IS_PAIRED_MATCH, indel_recorder, my_value_array_index, read1_txt , rl1 , INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! r_need_reverse, qual1_txt , FASTQ_FORMAT, dynamic_align_short, dynamic_align_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:587:45: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
allvote->max_final_quality[queries] = final_mapping_quality_edit(my_value_array_index, allvote->max_positions[queries], read1_txt, qual1_txt, cigar_str, FASTQ_FORMAT, &mismatch, rl1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:590:41: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
allvote->edit_distance[queries] = mismatch;
˜ ^˜˜˜˜˜˜˜
aligner.c:597:44: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
allvote->max_final_quality[queries] = final_mapping_quality_edit(my_value_array_index, allvote->max_positions[queries], read1_txt, qual1_txt, cigar_str, FASTQ_FORMAT, &mismatch,rl1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:598:40: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
allvote->edit_distance[queries] = mismatch;
˜ ^˜˜˜˜˜˜˜
aligner.c:686:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
queries = *processed_reads;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:737:86: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
subread_step = max(3.00001, (read_len-16-GENE_SLIDING_STEP)*1.0/(TOTAL_SUBREADS-1)+0.00001);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
aligner.c:737:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
subread_step = max(3.00001, (read_len-16-GENE_SLIDING_STEP)*1.0/(TOTAL_SUBREADS-1)+0.00001);
˜ ^˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
aligner.c:780:38: warning: implicit conversion changes signedness: 'int' to 'gehash_key_t' (aka 'unsigned int') [-Wsign-conversion]
gehash_key_t subread_integer = genekey2int(subread_string, ginp->space_type);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:795:226: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q_CtoT(my_table, subread_integer , subread_offset, read_len, is_counterpart , vote , 1 , 1, subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
aligner.c:797:195: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q(my_table, subread_integer , subread_offset, read_len, is_counterpart , vote , 1 , 1, subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
aligner.c:835:253: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
is_paired_match = select_positions_array(InBuff, read_len, InBuff2, read2_len,vote_read1, vote_read2, &numvote_read1, &numvote_read2, &sum_quality, &quality_read1, &quality_read2, read1_indel_recorder, read2_indel_recorder, &pos_read1, &pos_read2, MAX_PAIRED_DISTANCE, MIN_PAIRED_DISTANCE, ACCEPT_SUBREADS, ACCEPT_MINOR_SUBREADS, is_counterpart, my_value_array_index, ginp -> space_type, INDEL_TOLERANCE, NUMBER_OF_ANCHORS_PAIRED , QualityBuff, QualityBuff2, QUALITY_SCALE, allvote->max_indel_tolerance, & is_break_even, TOTAL_SUBREADS);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:835:274: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
is_paired_match = select_positions_array(InBuff, read_len, InBuff2, read2_len,vote_read1, vote_read2, &numvote_read1, &numvote_read2, &sum_quality, &quality_read1, &quality_read2, read1_indel_recorder, read2_indel_recorder, &pos_read1, &pos_read2, MAX_PAIRED_DISTANCE, MIN_PAIRED_DISTANCE, ACCEPT_SUBREADS, ACCEPT_MINOR_SUBREADS, is_counterpart, my_value_array_index, ginp -> space_type, INDEL_TOLERANCE, NUMBER_OF_ANCHORS_PAIRED , QualityBuff, QualityBuff2, QUALITY_SCALE, allvote->max_indel_tolerance, & is_break_even, TOTAL_SUBREADS);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:837:210: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
is_paired_match = select_positions(vote_read1, vote_read2, &numvote_read1, &numvote_read2, &sum_quality, &quality_read1, &quality_read2, &pos_read1, &pos_read2, read1_indel_recorder, read2_indel_recorder, MAX_PAIRED_DISTANCE, MIN_PAIRED_DISTANCE, ACCEPT_SUBREADS, ACCEPT_MINOR_SUBREADS, is_counterpart, NUMBER_OF_ANCHORS_PAIRED, allvote->max_indel_tolerance,& is_break_even);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:837:231: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
is_paired_match = select_positions(vote_read1, vote_read2, &numvote_read1, &numvote_read2, &sum_quality, &quality_read1, &quality_read2, &pos_read1, &pos_read2, read1_indel_recorder, read2_indel_recorder, MAX_PAIRED_DISTANCE, MIN_PAIRED_DISTANCE, ACCEPT_SUBREADS, ACCEPT_MINOR_SUBREADS, is_counterpart, NUMBER_OF_ANCHORS_PAIRED, allvote->max_indel_tolerance,& is_break_even);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:885:42: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
allvote->is_counterpart[queries*2] = is_counterpart;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:886:44: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
allvote->is_counterpart[queries*2+1] = is_counterpart;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:915:43: warning: implicit conversion changes signedness: 'gehash_data_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
add_allvote_q(allvote, queries*2 , pos_read1 , numvote_read1 , vote_read1->max_quality, is_counterpart, vote_read1->max_mask, vote_read1->max_indel_recorder, my_value_array_index, InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote_read1->max_coverage_end - vote_read1->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
aligner.c:915:364: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_allvote_q(allvote, queries*2 , pos_read1 , numvote_read1 , vote_read1->max_quality, is_counterpart, vote_read1->max_mask, vote_read1->max_indel_recorder, my_value_array_index, InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote_read1->max_coverage_end - vote_read1->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:917:43: warning: implicit conversion changes signedness: 'gehash_data_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
add_allvote_q(allvote, queries*2+1, pos_read2 , numvote_read2 , vote_read2->max_quality, is_counterpart, vote_read2->max_mask, vote_read2->max_indel_recorder, my_value_array_index, InBuff2, read2_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, is_counterpart, QualityBuff2, FASTQ_FORMAT, vote_read2->max_coverage_end - vote_read2->max_coverage_start, dynamic_align_short, dynamic_align_char,USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
aligner.c:917:366: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_allvote_q(allvote, queries*2+1, pos_read2 , numvote_read2 , vote_read2->max_quality, is_counterpart, vote_read2->max_mask, vote_read2->max_indel_recorder, my_value_array_index, InBuff2, read2_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, is_counterpart, QualityBuff2, FASTQ_FORMAT, vote_read2->max_coverage_end - vote_read2->max_coverage_start, dynamic_align_short, dynamic_align_char,USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:940:37: warning: implicit conversion changes signedness: 'int' to 'gehash_key_t' (aka 'unsigned int') [-Wsign-conversion]
gehash_key_t subread_integer = genekey2int(subread_string, ginp->space_type);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:953:242: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
total_results = gehash_go_q_CtoT (my_table, subread_integer , subread_offset , read_len, is_counterpart, vote , 1, 1 , subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
aligner.c:955:210: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
total_results = gehash_go_q(my_table, subread_integer , subread_offset , read_len, is_counterpart, vote , 1, 1 , subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
aligner.c:985:39: warning: implicit conversion changes signedness: 'gehash_data_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
add_allvote_q(allvote, queries, max_position , max_vote, max_quality, is_counterpart, max_mask, max_indel_recorder, my_value_array_index,InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote->max_coverage_end - vote->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
aligner.c:985:314: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_allvote_q(allvote, queries, max_position , max_vote, max_quality, is_counterpart, max_mask, max_indel_recorder, my_value_array_index,InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote->max_coverage_end - vote->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:990:45: warning: implicit conversion changes signedness: 'gehash_data_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
add_allvote_q(allvote, queries, vote->max_position , vote->max_vote, vote->max_quality , is_counterpart, vote->max_mask, vote->max_indel_recorder, my_value_array_index, InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote->max_coverage_end - vote->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
aligner.c:990:346: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_allvote_q(allvote, queries, vote->max_position , vote->max_vote, vote->max_quality , is_counterpart, vote->max_mask, vote->max_indel_recorder, my_value_array_index, InBuff, read_len, INDEL_TOLERANCE, TOTAL_SUBREADS, ginp->space_type, REPORT_POTENTIAL_JUNCTION_READS, ! is_counterpart, QualityBuff, FASTQ_FORMAT, vote->max_coverage_end - vote->max_coverage_start, dynamic_align_short, dynamic_align_char, USE_BASEINDEX_BREAK_TIE);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1012:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'long long' [-Wconversion]
long long int all_steps = (read_fsize*1.0/reads_density) * all_tables;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1015:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
long long int finished_steps = ((section_length)*table_no + base_number*all_tables+queries);
˜^˜˜˜˜˜˜˜
aligner.c:1020:110: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
print_running_log(finished_rate, reads_per_second, expected_seconds, (unsigned long long int)all_steps / all_tables, ginp2!=NULL);
˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:953:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
total_results = gehash_go_q_CtoT (my_table, subread_integer , subread_offset , read_len, is_counterpart, vote , 1, 1 , subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:955:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
total_results = gehash_go_q(my_table, subread_integer , subread_offset , read_len, is_counterpart, vote , 1, 1 , subread_quality, INDEX_THRESHOLD, INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1049:219: warning: implicit conversion changes signedness: 'unsigned long long' to 'long long' [-Wsign-conversion]
run_search(data_param->my_table, data_param->my_value_array_index, data_param->table_no, data_param->all_vote, data_param->ginp , data_param->ginp2, data_param->index_prefix, data_param->processed_reads, data_param->base_number, data_param->all_tables, data_param->input_data_lock, thid, data_param-> section_length);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
aligner.c:1054:222: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
run_final_stage(data_param -> array_index_set , data_param->all_vote , data_param-> ginp, data_param-> ginp2 , data_param-> processed_reads, data_param-> all_tables, data_param-> input_data_lock, thid, data_param-> section_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1067:38: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
unsigned long long int current_fp = ftello(ginp -> input_fp);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1078:17: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
current_fp2 = ftello(ginp2 -> input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1116:75: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
run_search(my_table, USE_VALUE_ARRAY_INDEX? &value_array_index : NULL, tabno, all_vote, ginp , ginp2, index_prefix, &processed_reads, base_number, all_tables, NULL /*the data lock is null*/, 0 /*I'm the 0-th thread*/, section_length);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
aligner.c:1116:138: warning: implicit conversion changes signedness: 'unsigned long long' to 'long long' [-Wsign-conversion]
run_search(my_table, USE_VALUE_ARRAY_INDEX? &value_array_index : NULL, tabno, all_vote, ginp , ginp2, index_prefix, &processed_reads, base_number, all_tables, NULL /*the data lock is null*/, 0 /*I'm the 0-th thread*/, section_length);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
aligner.c:1127:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
data_param.table_no = tabno;
˜ ^˜˜˜˜
aligner.c:1178:29: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:1180:31: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp2 -> input_fp, current_fp2, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
aligner.c:1185:107: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
run_final_stage(value_index_set , all_vote , ginp, ginp2 , & processed_reads, all_tables, NULL, 0, section_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1227:28: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:1229:30: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp2 -> input_fp, current_fp2, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
aligner.c:1238:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return processed_reads;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1529:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(init_allvote(&allvote, all_reads, INDEL_TOLERANCE )) return -1;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
aligner.c:1551:131: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
processed_reads_block = run_search_index(&ginp, read2_file[0] ? (&ginp2):NULL, index_prefix, &allvote, out_fp, processed_reads, all_tables, &succeed_reads);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
aligner.c:1554:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
processed_reads += processed_reads_block ;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1557:39: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
unsigned long long int current_fp = ftello(ginp.input_fp);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
aligner.c:1561:25: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp.input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
83 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c atgcContent.c -o atgcContent.o
atgcContent.c:62:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
atgcContent.c:52:7: warning: unused variable 'offset' [-Wunused-variable]
int offset;
^
atgcContent.c:51:7: warning: unused variable 'readlen' [-Wunused-variable]
int readlen;
^
atgcContent.c:48:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
atgcContent.c:54:7: warning: unused variable 'data_ready' [-Wunused-variable]
int data_ready=1;
^
atgcContent.c:49:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
atgcContent.c:100:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
atgcContent.c:90:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
atgcContent.c:89:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c detectionCall.c -o detectionCall.o
detectionCall.c:156:32: warning: unused variable 'read_entrezid' [-Wunused-variable]
int32_t read_start, read_end, read_entrezid, read_n, read_gc, read_at;
^
detectionCall.c:194:9: warning: unused variable 'z' [-Wunused-variable]
size_t z;
^
detectionCall.c:203:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
while ((readline = fgets(line, len, fin)) != NULL){
˜˜˜˜˜ ^˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:96:32: warning: unused variable 'read_length' [-Wunused-variable]
int32_t read_start, read_end, read_length;
^
detectionCallAnnotation.c:131:47: warning: unused variable 'read_length' [-Wunused-variable]
int32_t read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c:131:10: warning: unused variable 'read_entrezid' [-Wunused-variable]
int32_t read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c:181:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(line)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
detectionCallAnnotation.c:268:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
len = strlen(line)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c exon-algorithms.c -o exon-algorithms.o
exon-algorithms.c:33:81: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_matched_base = gvindex_match_base(my_array_index, potential_position+i+bias, base_int);
˜^
exon-algorithms.c:33:83: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_matched_base = gvindex_match_base(my_array_index, potential_position+i+bias, base_int);
˜^˜˜˜
exon-algorithms.c:34:49: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
read_matchingness[bias+indel_tolerance][i] = is_matched_base;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:103:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
arena -> read_lens = malloc(sizeof(short) * all_queries);
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:104:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
arena -> arenas = malloc(sizeof(struct gene_exon_arena) * all_queries);
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:116:33: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
arena -> read_lens[queries] = read_len ;
˜ ^˜˜˜˜˜˜˜
exon-algorithms.c:155:28: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
goodbases [min_index] = my_good_bases;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:158:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
is_good [min_index] = is_good_bound;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:163:18: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
goodbases[i] = my_good_bases;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:166:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
is_good[i] = is_good_bound;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:172:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero (arena -> read_lens, sizeof(short) * arena->max_len);
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜
exon-algorithms.c:199:23: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
best_total_len = value;
˜ ^˜˜˜˜
exon-algorithms.c:232:125: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
int is_exoned = match_read_exon(read_str, read_len, potential_position, my_array_index, indel_tolerance, & split_point, from_end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
exon-algorithms.c:243:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_good_b = is_good_boundary(potential_position + split_point,index, &potential_position, is_reversed);
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:261:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char c1 = gvindex_get(index, test_boundary+i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:261:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char c1 = gvindex_get(index, test_boundary+i);
˜^
exon-algorithms.c:262:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char c2 = gvindex_get(index, test_boundary+i+1);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-algorithms.c:262:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char c2 = gvindex_get(index, test_boundary+i+1);
˜^
18 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c exon-align.c -o exon-align.o
exon-align.c:19:31: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float accepted_support_rate = 0.3;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
exon-align.c:26:36: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float EXON_MAJOR_HALF_VOTES_RATE = 0.1;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
exon-align.c:27:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float EXON_MIN_HALF_VOTES_RATE = 0.15;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
exon-align.c:132:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best_pos1_list = (unsigned int * )malloc(sizeof(unsigned int)*items);
˜^˜˜˜˜
exon-align.c:133:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best_pos2_list = (unsigned int * )malloc(sizeof(unsigned int)*items);
˜^˜˜˜˜
exon-align.c:134:84: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best_vote1_list = (unsigned char * )malloc(sizeof(unsigned char)*items);
˜^˜˜˜˜
exon-align.c:135:84: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best_vote2_list = (unsigned char * )malloc(sizeof(unsigned char)*items);
˜^˜˜˜˜
exon-align.c:136:67: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> is_abnormal_list = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:137:67: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> is_reversed_list = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:138:68: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> half_marks_list = (short * )malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:139:70: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> splice_point_list = (short * )malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:140:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> splice_point_offset_1 = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:141:72: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> splice_point_offset_2 = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:142:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> indel_in_piece1 = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:143:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> indel_in_piece2 = (char * )malloc(sizeof(char)*items);
˜^˜˜˜˜
exon-align.c:145:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best1_read_start_pos = (short * )malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:146:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> best1_read_end_pos = (short * )malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:147:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> final_quality = (float *)malloc(sizeof(float)*items);
˜^˜˜˜˜
exon-align.c:148:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> read_coverage_start = (short *)malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:149:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> read_coverage_end = (short *)malloc(sizeof(short)*items);
˜^˜˜˜˜
exon-align.c:154:70: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
halves_record -> cigar_string_buffer = (char * )malloc(sizeof(char)*items*EXON_MAX_CIGAR_LEN);
˜^˜˜˜˜
exon-align.c:163:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote1_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:163:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote1_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:164:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote2_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:164:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote2_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:165:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> cigar_string_buffer , 0 , sizeof(char)*items*EXON_MAX_CIGAR_LEN);
˜^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:165:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> cigar_string_buffer , 0 , sizeof(char)*items*EXON_MAX_CIGAR_LEN);
˜^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:166:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> half_marks_list, 0, sizeof(short)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:166:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> half_marks_list, 0, sizeof(short)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:167:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece1 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:167:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece1 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:168:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece2 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:168:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece2 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:210:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote1_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:210:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote1_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:211:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote2_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:211:76: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> best_vote2_list, 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:212:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> half_marks_list, 0, sizeof(short)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:212:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> half_marks_list, 0, sizeof(short)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:213:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece1 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:213:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece1 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:214:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece2 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:214:77: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> indel_in_piece2 , 0, sizeof(char)*halves_record -> max_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:215:82: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> cigar_string_buffer , 0 , sizeof(char)*halves_record -> max_len*EXON_MAX_CIGAR_LEN);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
exon-align.c:215:82: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(halves_record -> cigar_string_buffer , 0 , sizeof(char)*halves_record -> max_len*EXON_MAX_CIGAR_LEN);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
exon-align.c:230:56: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
halves_record -> best1_read_start_pos[read_number] = best_pos_start;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:231:54: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
halves_record -> best1_read_end_pos[read_number] = best_pos_end;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:259:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char base = gvindex_get( my_value_array_index, pos + matching_position);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:259:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char base = gvindex_get( my_value_array_index, pos + matching_position);
^˜˜ ˜
exon-align.c:276:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
base = gvindex_get( my_value_array_index, pos + matching_position + OVERLAPPING_TEST_LENGTH);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:276:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
base = gvindex_get( my_value_array_index, pos + matching_position + OVERLAPPING_TEST_LENGTH);
^˜˜ ˜
exon-align.c:285:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
base = gvindex_get( my_value_array_index, pos + matching_position - OVERLAPPING_TEST_LENGTH);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:285:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
base = gvindex_get( my_value_array_index, pos + matching_position - OVERLAPPING_TEST_LENGTH);
^˜˜ ˜
exon-align.c:363:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
locate_gene_position(max_pos + read_len, &_global_offsets, &best_chro_name, &best_chro_pos);
˜ ^˜˜˜˜˜˜˜
exon-align.c:368:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
locate_gene_position(vote->pos[i][j] +read_len, &_global_offsets, &chro_name, &chro_pos);
˜^˜˜˜˜˜˜˜
exon-align.c:387:60: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
test_vote_value = 8888888 + vote->votes[i][j]* 1000000 - abs(dist);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
exon-align.c:541:65: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
repeat_record[repeated_pos] = (vote-> coverage_start[i][j] >> offset_shifting);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:542:65: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
repeat_record[repeated_pos+1] = (vote-> coverage_end[i][j] >> offset_shifting);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:543:59: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
repeat_record[repeated_pos+2] = (is_negative?0x80:0) | (vote->votes[i][j]&0x7f);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:553:65: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
repeat_record[repeated_pos] = (vote-> coverage_start[i][j] >> offset_shifting);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:554:65: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
repeat_record[repeated_pos+1] = (vote-> coverage_end[i][j] >> offset_shifting);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:555:59: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
repeat_record[repeated_pos+2] = (is_negative?0x80:0) | (vote->votes[i][j]&0x7f);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:676:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(h1_2ch, my_value_array_index, pos1 - indel_offset1+ bps_pos_x , is_reversed);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:676:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(h1_2ch, my_value_array_index, pos1 - indel_offset1+ bps_pos_x , is_reversed);
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:677:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(h2_2ch, my_value_array_index, pos2 - 2 - indel_offset2 + bps_pos_x, is_reversed);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:677:75: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(h2_2ch, my_value_array_index, pos2 - 2 - indel_offset2 + bps_pos_x, is_reversed);
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:702:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
first_exon_end = pos2 + bps_pos_x - indel_offset2;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:702:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
first_exon_end = pos2 + bps_pos_x - indel_offset2;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:702:42: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
first_exon_end = pos2 + bps_pos_x - indel_offset2;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:703:42: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
second_half_start = pos1 + bps_pos_x- indel_offset1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:703:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
second_half_start = pos1 + bps_pos_x- indel_offset1;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:703:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
second_half_start = pos1 + bps_pos_x- indel_offset1;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:705:87: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m1 = match_chro(read + break_point_half - donar_conf_len , my_value_array_index, first_exon_end, donar_conf_len, is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:706:87: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m2 = match_chro(read + break_point_half , my_value_array_index, second_half_start-donar_conf_len , donar_conf_len, is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:708:86: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
x1 = match_chro(read + break_point_half , my_value_array_index, first_exon_end - donar_conf_len, donar_conf_len , is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:709:88: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
x2 = match_chro(read + break_point_half - donar_conf_len , my_value_array_index, second_half_start , donar_conf_len, is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:713:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
first_exon_end = pos1 + bps_pos_x - indel_offset1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:713:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
first_exon_end = pos1 + bps_pos_x - indel_offset1;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:713:42: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
first_exon_end = pos1 + bps_pos_x - indel_offset1;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:714:43: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
second_half_start = pos2 + bps_pos_x - indel_offset2;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:714:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
second_half_start = pos2 + bps_pos_x - indel_offset2;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:714:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
second_half_start = pos2 + bps_pos_x - indel_offset2;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:716:100: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m1 = match_chro(read + break_point_half - donar_conf_len, my_value_array_index, first_exon_end-donar_conf_len , donar_conf_len, is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:717:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
m2 = match_chro(read + break_point_half , my_value_array_index, second_half_start, donar_conf_len, is_reversed, space_type);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:719:71: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
x1 = match_chro(read + break_point_half , my_value_array_index, first_exon_end, donar_conf_len , is_reversed,space_type);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:720:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
x2 = match_chro(read + break_point_half - donar_conf_len, my_value_array_index, second_half_start - donar_conf_len, donar_conf_len , is_reversed,space_type);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:786:63: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + group_anchor)) - NULL);
˜˜˜˜ ^
exon-align.c:786:80: warning: arithmetic on pointers to void is a GNU extension [-Wpointer-arith]
grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + group_anchor)) - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜
exon-align.c:793:32: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(pos_table, (NULL+(pos / EXON_GROUPING_SIZE)), (NULL +grouped_pos));
˜˜˜˜^
exon-align.c:793:68: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(pos_table, (NULL+(pos / EXON_GROUPING_SIZE)), (NULL +grouped_pos));
˜˜˜˜ ^
exon-align.c:810:42: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int max_piece_len = rl, max_grouped_pos=read_tail_pos;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:818:46: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
max_matched_bases_rate = (matched_bases)*1./effect_tested_len ;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:835:76: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + read_tail_pos - delta_pos)) - NULL);
˜˜˜˜ ^
exon-align.c:835:92: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + read_tail_pos - delta_pos)) - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
exon-align.c:835:106: warning: arithmetic on pointers to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + read_tail_pos - delta_pos)) - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜
exon-align.c:839:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int test_piece_len = read_tail_pos - grouped_pos;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:842:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matched_bases = match_indel_chro_to_back(read+rl-test_piece_len, my_value_array_index, read_tail_pos - test_piece_len, test_piece_len,&indels, &indel_point, EXON_INDEL_TOLERANCE, test_piece_len - rl);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:850:54: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float test_matched_bases_rate = (matched_bases)*1./effect_tested_len ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:853:84: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
connect_to_t * connect_to = (connect_to_t *)HashTableGet(connection_table, NULL+grouped_pos);
˜˜˜˜^
exon-align.c:861:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(connect_to_iii - (rl-test_piece_len) >= low_border && connect_to_iii < high_border)
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:868:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (accepted && (grouped_pos > read_tail_pos - rl + EXON_MIN_HALF_LENGTH/* -1*/)){
˜ ^˜
exon-align.c:868:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (accepted && (grouped_pos > read_tail_pos - rl + EXON_MIN_HALF_LENGTH/* -1*/)){
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:873:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
max_grouped_pos = grouped_pos;
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:887:63: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+1] = rl - max_piece_len + max_indels;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:888:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+3] = ((max_indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&( max_indels << 4)) + (max_piece_quality_good << 3);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:888:165: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+3] = ((max_indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&( max_indels << 4)) + (max_piece_quality_good << 3);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
exon-align.c:899:8: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (max_grouped_pos - connect_to_iii < 10)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:901:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(!(connect_to_iii - (rl-max_piece_len) >= low_border && connect_to_iii < high_border))
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:905:61: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+6] = rl + max_indels - max_piece_len;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:907:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int this_jump = max_grouped_pos - connect_to_iii;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:924:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases = match_indel_chro_to_back(read, my_value_array_index, read_tail_pos - rl, rl, &indels, &indel_point, EXON_INDEL_TOLERANCE, 0);
˜ ^˜
exon-align.c:931:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 3] = ((indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&(indels << 4)) + (max_piece_quality_good << 3);
^˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:931:160: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 3] = ((indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&(indels << 4)) + (max_piece_quality_good << 3);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
exon-align.c:951:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int max_grouped_pos = read_head_pos;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:961:46: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
max_matched_bases_rate = (matched_bases)*1./effect_tested_len;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:975:76: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + delta_pos + read_head_pos)) - NULL);
˜˜˜˜ ^
exon-align.c:975:88: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + delta_pos + read_head_pos)) - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
exon-align.c:975:106: warning: arithmetic on pointers to void is a GNU extension [-Wpointer-arith]
unsigned int grouped_pos = (unsigned int) (HashTableGet(pos_table, (NULL + delta_pos + read_head_pos)) - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜
exon-align.c:981:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int test_piece_len = grouped_pos - read_head_pos;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:995:54: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float test_matched_bases_rate = (matched_bases)*1./effect_tested_len;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:999:84: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
connect_to_t * connect_to = (connect_to_t *)HashTableGet(connection_table, NULL+grouped_pos);
˜˜˜˜^
exon-align.c:1007:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(connect_to_iii >= low_border && connect_to_iii + rl < high_border)
˜ ^˜
exon-align.c:1014:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (accepted && (grouped_pos < read_head_pos + rl - EXON_MIN_HALF_LENGTH/* +1*/)){
˜ ^˜
exon-align.c:1014:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (accepted && (grouped_pos < read_head_pos + rl - EXON_MIN_HALF_LENGTH/* +1*/)){
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1019:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
max_grouped_pos = grouped_pos;
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:1033:73: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+2] = full_rl - rl + max_piece_len - max_indels;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1034:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+3] = ((max_indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&( max_indels << 4)) + (max_piece_quality_good << 3);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:1034:166: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+3] = ((max_indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + (0xffff&( max_indels << 4)) + (max_piece_quality_good << 3);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
exon-align.c:1047:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (connect_to_iii - max_grouped_pos < 10)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1049:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(!(connect_to_iii >= low_border && connect_to_iii + rl < high_border))
˜ ^˜
exon-align.c:1053:71: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4+5] = full_rl - rl - max_indels + max_piece_len;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1061:51: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int this_jump_size = connect_to_iii - max_grouped_pos;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1082:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 2] = full_rl;
˜ ^˜˜˜˜˜˜
exon-align.c:1083:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 3] = ((indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + ((0xfff&indels) << 4) + (max_piece_quality_good << 3);
^˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:1083:128: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 3] = ((indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + ((0xfff&indels) << 4) + (max_piece_quality_good << 3);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
exon-align.c:1083:161: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cigar_recorder [number_of_piece * 4 + 3] = ((indel_point + cigar_recorder [number_of_piece*4+1]) << 16) + ((0xfff&indels) << 4) + (max_piece_quality_good << 3);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
exon-align.c:1138:85: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
my_range_end = min((int)(reads_per_thread*(1+thread_id) + 0.5 -1 ), processed_reads*(1+(ginp2!=NULL)));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:29: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
exon-align.c:1191:88: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Second Iteration", i*EXON_ALL_THREADS*1./(1+(ginp2!=NULL))/processed_reads, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1247:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
explain_buff [0] = pos + b_search_tail;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1248:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
explain_buff [2] = b_search_tail;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1257:100: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
junction_tree_b_explorer(bed_table, pos_table, connection_table, inb , b_search_tail, rl , pos + b_search_tail + halves_record ->indel_in_piece1[i] , 0, explain_buff, 0, &result_total_matched_bases , explain_result, &result_number_pieces, my_value_array_index, ginp, f_search_head, qualityb, EXON_FASTQ_FORMAT, match_score, 0, &max_jump_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1257:116: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
junction_tree_b_explorer(bed_table, pos_table, connection_table, inb , b_search_tail, rl , pos + b_search_tail + halves_record ->indel_in_piece1[i] , 0, explain_buff, 0, &result_total_matched_bases , explain_result, &result_number_pieces, my_value_array_index, ginp, f_search_head, qualityb, EXON_FASTQ_FORMAT, match_score, 0, &max_jump_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1327:76: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
explain_result[4*j] -= (explain_result[4*j+2]-explain_result[4*j+1] + indels_in_section);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1332:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (total_pieces >0)f_search_head = explain_result[(total_pieces-1)*4 + 1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1335:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
explain_buff [1] = f_search_head;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1403:46: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
halves_record -> best_vote2_list[i]= max(MIN_VOTE2_TMP_VAR, halves_record -> best_vote2_list[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:1426:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int len_p1 = indel_pos - explain_result[ 4*j+1] , len_p2 = explain_result[ 4*j+2] - indel_pos +min(0, indel_length);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1426:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int len_p1 = indel_pos - explain_result[ 4*j+1] , len_p2 = explain_result[ 4*j+2] - indel_pos +min(0, indel_length);
^˜˜˜˜˜˜˜˜ ˜
exon-align.c:1426:102: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int len_p1 = indel_pos - explain_result[ 4*j+1] , len_p2 = explain_result[ 4*j+2] - indel_pos +min(0, indel_length);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1426:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int len_p1 = indel_pos - explain_result[ 4*j+1] , len_p2 = explain_result[ 4*j+2] - indel_pos +min(0, indel_length);
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:1426:110: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int len_p1 = indel_pos - explain_result[ 4*j+1] , len_p2 = explain_result[ 4*j+2] - indel_pos +min(0, indel_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:29: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
exon-align.c:1462:131: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
sprintf (cigar_piece, "%dN",explain_result[4*j+4]- (explain_result[ 4*j] + explain_result[ 4*j+2] - explain_result[4*j+1] + indel_length));
˜ ^˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^
exon-align.c:1504:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_small = min(explain_result[4*j] + explain_result[4*j+2] - explain_result[4*j+1] + this_step_indels, explain_result[4*j+4]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:21: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
exon-align.c:1504:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_small = min(explain_result[4*j] + explain_result[4*j+2] - explain_result[4*j+1] + this_step_indels, explain_result[4*j+4]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:33: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
exon-align.c:1505:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_big = max(explain_result[4*j] + explain_result[4*j+2] - explain_result[4*j+1] + this_step_indels, explain_result[4*j+4]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:21: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:1505:105: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_big = max(explain_result[4*j] + explain_result[4*j+2] - explain_result[4*j+1] + this_step_indels, explain_result[4*j+4]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:1517:47: warning: implicit conversion loses integer precision: 'unsigned int' to 'short' [-Wconversion]
short left_len = explain_result[4*j+2] - explain_result[4*j+1];
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1518:48: warning: implicit conversion loses integer precision: 'unsigned int' to 'short' [-Wconversion]
short right_len = explain_result[4*j+6] - explain_result[4*j+5];
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1521:40: warning: operand of ? changes signedness: 'short' to 'unsigned short' [-Wsign-conversion]
search_res -> left_extend = max(left_len, search_res -> left_extend);
˜ ^˜˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:1522:41: warning: operand of ? changes signedness: 'short' to 'unsigned short' [-Wsign-conversion]
search_res -> right_extend = max(right_len, search_res -> right_extend);
˜ ^˜˜˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:1644:52: warning: arithmetic on pointers to void is a GNU extension [-Wpointer-arith]
unsigned int pos = (unsigned int)(cursor -> key - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜
exon-align.c:1646:38: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
if(!HashTableContainsKey(old, NULL+pos))
˜˜˜˜^
exon-align.c:1647:27: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(old, NULL+pos , NULL+pos);
˜˜˜˜^
exon-align.c:1647:38: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(old, NULL+pos , NULL+pos);
˜˜˜˜^
exon-align.c:1668:52: warning: arithmetic on pointers to void is a GNU extension [-Wpointer-arith]
unsigned int pos = (unsigned int)(cursor -> key - NULL);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜
exon-align.c:1670:55: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
connect_to_t * connect_old = HashTableGet(old, NULL+pos);
˜˜˜˜^
exon-align.c:1706:27: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(old, NULL+pos, cursor-> value);
˜˜˜˜^
exon-align.c:1778:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
nbkey.big_key = p->big_key + indels + delta;
˜ ^˜˜˜˜˜
exon-align.c:1778:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
nbkey.big_key = p->big_key + indels + delta;
˜ ^˜˜˜˜
exon-align.c:1779:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
nbkey.small_key = p->small_key + delta;
˜ ^˜˜˜˜
exon-align.c:1810:67: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
connect_to_t * next_jump = HashTableGet(connection_table, (NULL+c0));
˜˜˜˜^
exon-align.c:1830:39: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTableRemove(pos_table, (NULL+c0));
˜˜˜˜^
exon-align.c:1831:46: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTableRemove(connection_table, (NULL+c0));
˜˜˜˜^
exon-align.c:1984:67: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
connect_to = (connect_to_t *)HashTableGet(connection_table, NULL + p1);
˜˜˜˜ ^
exon-align.c:1989:32: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
connect_to-> i_am_reversed = is_p1_reversed;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:1990:39: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
HashTablePut(connection_table, NULL + p1, connect_to);
˜˜˜˜ ^
exon-align.c:2011:41: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
connect_to ->is_opposite_reversed[i] = is_p2_reversed;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2079:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(match_chro(inb, base_index, pos_small + delta_pos, SHORT_EXON_MIN_LENGTH , 0, space_type) >= SHORT_EXON_MIN_LENGTH*.7)
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:2094:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(cc, base_index, pos_small + test_donor_pos, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2114:70: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
new_pos = match_chro_range(inb, base_index, new_pos, 7 , new_pos - test_end , SEARCH_BACK);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
exon-align.c:2126:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(cc, base_index, pos_small + splice_point -2, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2129:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(cc2, base_index, new_pos + splice_point, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2132:88: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_in_exon_old = match_chro(inb + splice_point, base_index, pos_small + splice_point , SHORT_EXON_WINDOW , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2136:98: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
test_score = 1000000+ (matched_in_exon_new )*10000 + matched_in_exon_old * 1000 + new_pos - test_end;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
exon-align.c:2136:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
test_score = 1000000+ (matched_in_exon_new )*10000 + matched_in_exon_old * 1000 + new_pos - test_end;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:2143:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
best_j1_edge = new_pos + splice_point;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2144:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
best_j2_edge = pos_small + splice_point;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2204:102: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(SHORT_EXON_MIN_LENGTH *0.6 < match_chro(inb + rl - SHORT_EXON_MIN_LENGTH, base_index, pos_big + rl - SHORT_EXON_MIN_LENGTH , SHORT_EXON_MIN_LENGTH , 0, space_type))
˜ ^˜
exon-align.c:2211:75: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(match_chro(inb + rl - SHORT_EXON_MIN_LENGTH, base_index, pos_big + rl - SHORT_EXON_MIN_LENGTH + delta_pos, SHORT_EXON_MIN_LENGTH , 0, space_type) >= SHORT_EXON_MIN_LENGTH*.7)
˜ ^˜
exon-align.c:2211:104: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(match_chro(inb + rl - SHORT_EXON_MIN_LENGTH, base_index, pos_big + rl - SHORT_EXON_MIN_LENGTH + delta_pos, SHORT_EXON_MIN_LENGTH , 0, space_type) >= SHORT_EXON_MIN_LENGTH*.7)
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:2226:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(cc, base_index, pos_big + test_donor_pos, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2243:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int new_pos = pos_big +rl - SHORT_EXON_MIN_LENGTH +16;
˜^˜
exon-align.c:2247:100: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
new_pos = match_chro_range(inb + rl - SHORT_EXON_MIN_LENGTH, base_index, new_pos, 7 , test_end - new_pos , SEARCH_FRONT);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
exon-align.c:2260:67: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int new_pos_tail = (new_pos + SHORT_EXON_MIN_LENGTH -rl + splice_point);
˜^˜
exon-align.c:2260:72: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int new_pos_tail = (new_pos + SHORT_EXON_MIN_LENGTH -rl + splice_point);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2262:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
get_chro_2base(cc, base_index, pos_big + splice_point, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2269:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_in_exon_old = match_chro(inb + splice_point - SHORT_EXON_WINDOW , base_index, pos_big + splice_point - SHORT_EXON_WINDOW , SHORT_EXON_WINDOW, 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2271:98: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
test_score = 1000000+ (matched_in_exon_new)*10000 + matched_in_exon_old * 1000 + test_end - new_pos;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
exon-align.c:2271:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
test_score = 1000000+ (matched_in_exon_new)*10000 + matched_in_exon_old * 1000 + test_end - new_pos;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
exon-align.c:2278:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
best_j1_edge = pos_big + splice_point;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2351:23: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
my_range_start = max((int)(reads_per_thread * thread_id - 0.5),0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
exon-align.c:2352:21: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
my_range_end = min((int)(reads_per_thread*(1+thread_id) + 0.5), processed_reads*(1+(ginp2!=NULL)));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:33: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
exon-align.c:2357:7: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
i = my_range_start;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2388:88: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("First Iteration", i* EXON_ALL_THREADS*1./(1+(ginp2!=NULL))/processed_reads, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2483:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
is_accepted = test_donor(inb, rl, min(pos, pos2), max(pos,pos2), guess_break_point, negative_strand, test_range, is_soft_condition, EXON_INDEL_TOLERANCE, &test_real_break_point, my_value_array_index, indel_offset1, indel_offset2, negative_strand, ginp->space_type, halves_record ->best_vote2_list[i], &test_donor_score, &is_GTAG);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2504:49: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
halves_record ->splice_point_offset_1[i] = best_indel_p1;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2505:49: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
halves_record ->splice_point_offset_2[i] = best_indel_p2;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2511:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
is_accepted = test_donor(inb, rl, min(pos, pos2), max(pos,pos2), guess_break_point, negative_strand, test_range, is_soft_condition, EXON_INDEL_TOLERANCE, &real_break_point, my_value_array_index,0,0, negative_strand, ginp->space_type, halves_record ->best_vote2_list[i], &best_donor_score, & best_GTAG);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2544:97: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int m1 = match_chro(inb+p1_offset, my_value_array_index, halves_record -> best_pos1_list[i]+c1_offset , rl -20, (halves_record ->half_marks_list[i] & IS_NEGATIVE_STRAND_R1)?1:0, ginp->space_type);
˜^˜˜˜˜˜˜˜˜
exon-align.c:2545:97: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int m2 = match_chro(inb+p2_offset, my_value_array_index, halves_record -> best_pos2_list[i]+c2_offset , rl -20, (halves_record ->half_marks_list[i] & IS_NEGATIVE_STRAND_R2)?1:0, ginp->space_type);
˜^˜˜˜˜˜˜˜˜
exon-align.c:2558:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R1 = real_break_point+ halves_record -> best_pos1_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos1:indel_offset_pos2);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2558:161: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R1 = real_break_point+ halves_record -> best_pos1_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos1:indel_offset_pos2);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2558:179: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R1 = real_break_point+ halves_record -> best_pos1_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos1:indel_offset_pos2);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2559:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R2 = real_break_point+ halves_record -> best_pos2_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos2:indel_offset_pos1);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2559:161: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R2 = real_break_point+ halves_record -> best_pos2_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos2:indel_offset_pos1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2559:179: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R2 = real_break_point+ halves_record -> best_pos2_list[i] - (( halves_record -> best_pos1_list[i] < halves_record -> best_pos2_list[i] )?indel_offset_pos2:indel_offset_pos1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2563:45: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
halves_record -> splice_point_list[i] = real_break_point;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2789:69: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Saving results", i*1./(1+(ginp2!=NULL))/processed_reads, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2864:22: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
mapping_quality = halves_record -> final_quality[i] ;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:2955:69: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Saving results", i*1./(1+(ginp2!=NULL))/processed_reads, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3006:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_pos = old_pos * 10 + (cc-'0');
˜ ˜˜^˜˜˜
exon-align.c:3021:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag2 = old_flag;
˜ ^˜˜˜˜˜˜˜
exon-align.c:3022:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_quality2 = old_quality;
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:3027:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag1 = old_flag;
˜ ^˜˜˜˜˜˜˜
exon-align.c:3028:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_quality1 = old_quality;
˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:3140:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pos = halves_record -> is_reversed_list[i]? (pos + rl):(pos);
˜ ^˜
exon-align.c:3147:24: warning: implicit conversion turns floating-point number into integer: 'float' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
mapping_quality = halves_record -> final_quality[i] ;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3156:22: warning: implicit conversion changes signedness: 'gene_quality_score_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
old_quality2 = mapping_quality;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3174:22: warning: implicit conversion changes signedness: 'gene_quality_score_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
old_quality1 = mapping_quality;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3283:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag1 &= ˜SAM_FLAG_MATCHED_IN_PAIR;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3284:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag2 &= ˜SAM_FLAG_MATCHED_IN_PAIR;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3301:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag1 &= ˜SAM_FLAG_MATCHED_IN_PAIR;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3302:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag2 &= ˜SAM_FLAG_MATCHED_IN_PAIR;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3306:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag1 &= ˜SAM_FLAG_MATE_UNMATCHED;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3311:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag2 &= ˜SAM_FLAG_MATE_UNMATCHED;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3318:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag2 &= ˜SAM_FLAG_MATE_REVERSE_STRAND_MATCHED;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3323:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
old_flag1 &= ˜SAM_FLAG_MATE_REVERSE_STRAND_MATCHED;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3274:12: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
tlen = pair_dist;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:3403:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int windows = full_rl / EXON_LARGE_WINDOW +1;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
exon-align.c:3403:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int windows = full_rl / EXON_LARGE_WINDOW +1;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3404:62: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float overlap = (1.0*windows * EXON_LARGE_WINDOW - full_rl) / (windows-1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3413:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
read_len = full_rl -window_cursor;
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3413:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
read_len = full_rl -window_cursor;
˜^˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3415:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float subread_step = 3.00001;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
exon-align.c:3438:36: warning: implicit conversion changes signedness: 'int' to 'gehash_key_t' (aka 'unsigned int') [-Wsign-conversion]
gehash_key_t subread_integer = genekey2int(subread_string, color_space);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3443:108: warning: implicit conversion from 'double' to 'gene_quality_score_t' (aka 'int') changes value from 21.9 to 21 [-Wliteral-conversion]
gehash_go_q_CtoT(my_table, subread_integer , subread_offset, read_len,negative_strand, vote_p1, 1, 1, 21.9, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, EXON_MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
exon-align.c:3443:223: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q_CtoT(my_table, subread_integer , subread_offset, read_len,negative_strand, vote_p1, 1, 1, 21.9, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, EXON_MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
exon-align.c:3445:103: warning: implicit conversion from 'double' to 'gene_quality_score_t' (aka 'int') changes value from 21.9 to 21 [-Wliteral-conversion]
gehash_go_q(my_table, subread_integer , subread_offset, read_len,negative_strand, vote_p1, 1, 1, 21.9, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
exon-align.c:3445:187: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q(my_table, subread_integer , subread_offset, read_len,negative_strand, vote_p1, 1, 1, 21.9, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
exon-align.c:3471:119: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
int is_accepted = test_donor(InBuff, read_len, min(best_pos1, best_pos2), max(best_pos1,best_pos2), splice_point, negative_strand, read_len/4, 0, EXON_INDEL_TOLERANCE, &test_real_break_point, my_value_array_index, 0, 0, negative_strand, color_space, halves_record ->best_vote2_list[i], &test_donor_score, &is_GTAG);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3474:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R1 = test_real_break_point+ best_pos1;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3475:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int pos_R2 = test_real_break_point+ best_pos2;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3594:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'long long' [-Wconversion]
long long int all_steps = (read_fsize*1.0/reads_density) * all_tables;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3597:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
long long int finished_steps = ((section_length)*table_no + base_number*all_tables+queries);
˜^˜˜˜˜˜˜˜
exon-align.c:3602:111: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
print_running_log(finished_rate, reads_per_second, expected_seconds, (unsigned long long int)all_steps / all_tables, ginp2 != NULL);
˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:3639:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
queries = *processed_reads;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3667:48: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
halves_record -> best_vote1_list[qindex] = sam_qual1 ;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:3672:60: warning: implicit conversion turns floating-point number into integer: 'double' to 'short' [-Wconversion]
halves_record -> best1_read_end_pos[qindex] = read_len * 0.9;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
exon-align.c:3673:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'short' [-Wconversion]
halves_record -> best1_read_start_pos[qindex] = read_len * 0.1;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
exon-align.c:3679:49: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
halves_record -> best_vote1_list[qindex] = sam_qual2 ;
˜ ^˜˜˜˜˜˜˜˜
exon-align.c:3684:62: warning: implicit conversion turns floating-point number into integer: 'double' to 'short' [-Wconversion]
halves_record -> best1_read_end_pos[qindex] = read2_len * 0.9;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
exon-align.c:3685:64: warning: implicit conversion turns floating-point number into integer: 'double' to 'short' [-Wconversion]
halves_record -> best1_read_start_pos[qindex] = read2_len * 0.1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
exon-align.c:3765:69: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
if(tolerable_scan && (!EXON_NO_TOLERABLE_SCAN)) subread_step = 3.00001;
˜ ^˜˜˜˜˜˜
exon-align.c:3767:66: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
subread_step = (int)((read_len - 18)*1./(TOTAL_SUBREADS-1))+0.000001;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
exon-align.c:3781:38: warning: implicit conversion changes signedness: 'int' to 'gehash_key_t' (aka 'unsigned int') [-Wsign-conversion]
gehash_key_t subread_integer = genekey2int(subread_string, ginp->space_type);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3784:229: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q_CtoT(my_table, subread_integer , subread_offset, current_rlen, is_reversed, current_vote, 1, 1, 22, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, EXON_MAX_METHYLATION_C_NUMBER, low_border, high_border - current_rlen);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3786:193: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q(my_table, subread_integer , subread_offset, current_rlen, is_reversed, current_vote, 1, 1, 22, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, low_border, high_border - current_rlen);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3804:182: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_paired_match = select_positions(vote_p1, vote_p2, &numvote_read1, &numvote_read2, &sum_quality, &qual_r1, &qual_r2, &pos_read1, &pos_read2, record_index1, record_index2, EXON_MAX_PAIRED_DISTANCE, EXON_MIN_PAIRED_DISTANCE, 3, ACCEPT_MINOR_SUBREADS, is_reversed, EXON_NUMBER_OF_ANCHORS_PAIRED, EXON_INDEL_TOLERANCE, &is_breakeven);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3804:208: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_paired_match = select_positions(vote_p1, vote_p2, &numvote_read1, &numvote_read2, &sum_quality, &qual_r1, &qual_r2, &pos_read1, &pos_read2, record_index1, record_index2, EXON_MAX_PAIRED_DISTANCE, EXON_MIN_PAIRED_DISTANCE, 3, ACCEPT_MINOR_SUBREADS, is_reversed, EXON_NUMBER_OF_ANCHORS_PAIRED, EXON_INDEL_TOLERANCE, &is_breakeven);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3827:69: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, 2*queries+is_second_read, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:3827:81: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, 2*queries+is_second_read, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:3827:105: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, 2*queries+is_second_read, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3827:125: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, 2*queries+is_second_read, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3834:83: warning: implicit conversion changes signedness: 'gene_vote_number_t' (aka 'char') to 'unsigned char' [-Wsign-conversion]
halves_record -> best_vote1_list[queries*2+is_second_read] = current_vote->max_vote ;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
exon-align.c:3837:70: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
halves_record -> is_reversed_list[queries*2+is_second_read] = is_reversed_halves;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3851:202: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
fragile_junction_voting(bed_table, pos_table, connection_table, my_table, my_value_array_index , table_no, halves_record, is_second_read?InBuff2:InBuff, is_second_read?QualityBuff2:QualityBuff, current_rlen , is_reversed, ginp->space_type, low_border, high_border, vote_p3);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3861:69: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
if(tolerable_scan && (!EXON_NO_TOLERABLE_SCAN) ) subread_step = 3.00001;
˜ ^˜˜˜˜˜˜
exon-align.c:3863:66: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
subread_step = (int)((read_len - 18)*1./(TOTAL_SUBREADS-1)) + 0.00001;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
exon-align.c:3877:37: warning: implicit conversion changes signedness: 'int' to 'gehash_key_t' (aka 'unsigned int') [-Wsign-conversion]
gehash_key_t subread_integer = genekey2int(subread_string, ginp->space_type);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3881:219: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q_CtoT(my_table, subread_integer , subread_offset, read_len, is_reversed, vote_p1, 1, 1, 22, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, EXON_MAX_METHYLATION_C_NUMBER, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
exon-align.c:3883:183: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gehash_go_q(my_table, subread_integer , subread_offset, read_len, is_reversed, vote_p1, 1, 1, 22, INDEX_THRESHOLD, EXON_INDEL_TOLERANCE, subread_no, low_border, high_border - read_len);
˜ ^˜˜˜˜˜˜˜
exon-align.c:3911:68: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, queries, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:3911:80: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, queries, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:3911:104: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, queries, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3911:124: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
add_best_matching_halves(halves_record, best_pos1, best_pos2, best_vote1, best_vote2,is_abnormal, is_reversed_halves, splice_point, half_marks, queries, max_cover_start, max_cover_end, read_coverage_start, read_coverage_end, indel_in_p1, indel_in_p2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3919:60: warning: implicit conversion changes signedness: 'gene_vote_number_t' (aka 'char') to 'unsigned char' [-Wsign-conversion]
halves_record -> best_vote1_list[queries] = vote_p1->max_vote ;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
exon-align.c:3922:52: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
halves_record -> is_reversed_list[queries] = is_reversed_halves;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:3933:149: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
fragile_junction_voting(bed_table, pos_table, connection_table, my_table, my_value_array_index , table_no, halves_record, InBuff, QualityBuff, read_len , is_reversed, ginp->space_type, low_border, high_border, vote_p3);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
exon-align.c:3961:305: warning: implicit conversion changes signedness: 'unsigned long long' to 'long long' [-Wsign-conversion]
run_exon_search(data_param-> bed_table, data_param->pos_table, data_param->connection_table, data_param->my_table, data_param->my_value_array_index, data_param->table_no, data_param->halves_record, data_param->ginp , data_param->ginp2, data_param->index_prefix, data_param->processed_reads, data_param->base_number, data_param->all_tables, data_param->input_data_lock, thid, data_param-> section_length, data_param -> tolerable_scan);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
exon-align.c:3977:38: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
unsigned long long int current_fp = ftello(ginp -> input_fp);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4020:97: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
run_exon_search(overall_exon_bed, pos_table,connection_table, my_table, &value_array_index, tabno, halves_record, ginp , ginp2, index_prefix, &processed_reads, base_number, all_tables, NULL /*the data lock is null*/, 0 /*I'm the 0-th thread*/, section_length, tolerable_scan);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
exon-align.c:4020:165: warning: implicit conversion changes signedness: 'unsigned long long' to 'long long' [-Wsign-conversion]
run_exon_search(overall_exon_bed, pos_table,connection_table, my_table, &value_array_index, tabno, halves_record, ginp , ginp2, index_prefix, &processed_reads, base_number, all_tables, NULL /*the data lock is null*/, 0 /*I'm the 0-th thread*/, section_length, tolerable_scan);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:4031:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
data_param.table_no = tabno;
˜ ^˜˜˜˜
exon-align.c:4070:17: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
last_fp_pos = ftello(ginp -> input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4073:28: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:4102:29: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:4114:28: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:4129:27: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp -> input_fp, last_fp_pos, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
exon-align.c:4132:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return processed_reads;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4305:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = fgetc(fp);
˜˜˜ ^˜˜˜˜˜˜˜˜
exon-align.c:4315:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chro_pos1 += l_ext;
˜˜ ^˜˜˜˜
exon-align.c:4316:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chro_pos2 -= r_ext;
˜˜ ^˜˜˜˜
exon-align.c:4338:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
search_res->strand = is_reverse_strand;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4377:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chro_pos1 = chro_pos1*10 + (nch-'0');
˜ ˜˜˜^˜˜˜
exon-align.c:4379:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chro_pos2 = chro_pos2*10 + (nch-'0');
˜ ˜˜˜^˜˜˜
exon-align.c:4436:31: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
EXON_MAJOR_HALF_VOTES_RATE = .2;
˜ ^˜
exon-align.c:4489:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
EXON_MAJOR_HALF_VOTES_RATE = atof(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4718:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(init_halves_record(&halves_record, all_reads)) return -1;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
exon-align.c:4756:144: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int new_processed_reads = run_exon_search_index(&ginp, read2_file[0] ? (&ginp2):NULL, index_prefix, &halves_record, out_fp, processed_reads, all_tables, &succeed_reads, bed_index, pos_index, connection_index);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:4759:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
processed_reads += new_processed_reads;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4763:39: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
unsigned long long int current_fp = ftello(ginp.input_fp);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
exon-align.c:4768:25: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
fseeko(ginp.input_fp, current_fp, SEEK_SET);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
exon-align.c:4591:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for(xx=strlen(cwd);xx>=0; xx--)
˜^˜˜˜˜˜˜˜˜˜˜
313 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fullscan.c -o fullscan.o
fullscan.c:11:29: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float MIN_REPORTING_RATIO = 0.8;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fullscan.c:94:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
for(; current_pos + read_len < index.start_point + index.length ; current_pos++)
˜ ^˜˜˜˜˜˜˜
fullscan.c:97:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = gvindex_get(&index, current_pos + read_len);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fullscan.c:97:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char nch = gvindex_get(&index, current_pos + read_len);
˜ ^˜˜˜˜˜˜˜
fullscan.c:103:53: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Scan:", current_pos*1./SCAN_TOTAL_BASES, 80, &ic);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fullscan.c:63:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int read_len = strlen(read_str);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fullscan.c:121:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
while ((c = getopt (argc, argv, "i:m:?")) != -1)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fullscan.c:128:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
MIN_REPORTING_RATIO = atof(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
fullscan.c:142:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
argv[optind][i] = toupper(argv[optind][i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c:42:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
unsigned char * big_margin_rec = all_big_margin_rec+sizeof(int)*qid;
˜^˜˜
gene-algorithms.c:60:67: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
unsigned char * big_margin_rec = all_big_margin_rec+ sizeof(int)*query_id;
˜^˜˜˜˜˜˜˜
gene-algorithms.c:80:34: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
big_margin_rec[replace_id] = vote_n;
˜ ^˜˜˜˜˜
gene-algorithms.c:94:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = fgetc(fp);
˜ ^˜˜˜˜˜˜˜˜
gene-algorithms.c:103:11: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
return nch;
˜˜˜˜˜˜ ^˜˜
gene-algorithms.c:139:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return qual*1./testlen;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:157:23: warning: implicit conversion turns floating-point number into integer: 'float' to 'int' [-Wconversion]
return (rl - ret*3/4)*match_score;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:203:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'gene_quality_score_t' (aka 'int') [-Wconversion]
return ret/16000000.;
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜˜
gene-algorithms.c:217:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for(i=strlen(outbuff); i<105; i++)
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:225:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int bar_width = width - 7 - strlen(hint) , i;
˜˜˜˜˜˜^˜˜ ˜
gene-algorithms.c:230:25: warning: for loop has empty body [-Wempty-body]
for (i=0; i<width; i++);
^
gene-algorithms.c:230:25: note: put the semicolon on a separate line to silence this warning
gene-algorithms.c:225:28: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int bar_width = width - 7 - strlen(hint) , i;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:351:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (chrono>1)return offsets[chrono-1]+offset;
˜^˜˜˜˜˜
gene-algorithms.c:352:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return offset;
˜˜˜˜˜˜ ^˜˜˜˜˜
gene-algorithms.c:372:7: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(rl + linear >= offsets->read_offset[n]) return 1;
^˜ ˜
gene-algorithms.c:463:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
*position_result = vote->pos[max_index>>16][max_index&0xffff];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:471:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(allvote -> max_votes, allvote -> max_len* sizeof(*allvote -> max_votes));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:472:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(allvote -> masks, allvote -> max_len* sizeof(*allvote -> masks));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:473:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(allvote -> span_coverage , allvote -> max_len* sizeof(char));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:474:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(allvote -> big_margin_votes_shared, allvote -> max_len* sizeof(char));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:475:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(allvote -> edit_distance , allvote -> max_len* sizeof(short));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
gene-algorithms.c:499:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
allvote -> max_positions = (unsigned int *) malloc(sizeof(int)*expected_len);
˜^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:500:83: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> max_votes = (gene_vote_number_t *) calloc(sizeof(gene_vote_number_t), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:501:89: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> max_quality = (gene_quality_score_t *) calloc(sizeof(gene_quality_score_t), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:502:95: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> max_final_quality = (gene_quality_score_t *) calloc(sizeof(gene_quality_score_t), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:505:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> masks = (short *) calloc(sizeof(short), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:509:55: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> is_counterpart = (unsigned char *) malloc(expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:511:35: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
allvote -> max_indel_tolerance = allowed_indels;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:512:61: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
allvote -> indel_recorder_length = max(3*(allowed_indels+1)+1, 28);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-algorithms.c:513:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> span_coverage = (char *)calloc(sizeof(char), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:514:69: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> edit_distance = (unsigned short *)calloc(sizeof(short), expected_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:521:84: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
allvote -> max_indel_recorder = (char *)malloc( allvote -> indel_recorder_length *expected_len);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:542:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int cigar_len = strlen(cigar);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:574:19: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
*pos_offset = tmpv;
˜ ^˜˜˜
gene-algorithms.c:769:36: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
allvote -> is_counterpart[qid] = is_counterpart;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:770:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
allvote -> max_positions[qid] = pos;
˜ ^˜˜
gene-algorithms.c:812:36: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float EXON_RECOVER_MATCHING_RATE = 0.9;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
gene-algorithms.c:813:39: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float EXON_INDEL_MATCHING_RATE_TAIL = 0.8;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
gene-algorithms.c:814:39: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float EXON_INDEL_MATCHING_RATE_HEAD = 0.8;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
gene-algorithms.c:876:39: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
EXON_INDEL_MATCHING_RATE_HEAD = 0.85;
˜ ^˜˜˜
gene-algorithms.c:879:43: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
else EXON_INDEL_MATCHING_RATE_HEAD = 0.92;
˜ ^˜˜˜
gene-algorithms.c:893:39: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
EXON_INDEL_MATCHING_RATE_TAIL = 0.85;
˜ ^˜˜˜
gene-algorithms.c:896:43: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
else EXON_INDEL_MATCHING_RATE_TAIL = 0.92;
˜ ^˜˜˜
gene-algorithms.c:903:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
is_full_covered = extend_covered_region(array_index, pos, read_txt, read_len, cover_start, cover_end, 4, head_must_correct, tail_must_correct, max_indel, space_type, max_indel_recorder[k-1], &head_indel_pos, &head_indel_movement, &tail_indel_pos, &tail_indel_movement, is_head_high_quality, qual_txt, phred_version);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
gene-algorithms.c:907:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
allvote -> max_positions[qid] = pos;
˜ ^˜˜
gene-algorithms.c:917:79: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
*(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xff ;
˜ ^˜˜˜
gene-algorithms.c:992:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
moves = dynamic_align (read_txt + black_base_start, black_base_end-black_base_start , array_index, pos + blackref_base_start, max_indel, indel_operations, exp_indel, -10, black_base_end - black_base_start+5, dynamic_programming_short, dynamic_programming_char);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1035:22: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_operation = current_operation;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1068:79: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
*(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfd;
˜ ^˜˜˜
gene-algorithms.c:1095:79: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
*(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfe ;
˜ ^˜˜˜
gene-algorithms.c:984:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int vpos = strlen(tmp_cigar);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1012:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int vpos = strlen(tmp_cigar);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1021:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int vpos = strlen(tmp_cigar);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1042:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int vpos = strlen(tmp_cigar);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1065:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int vpos = strlen(tmp_cigar);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1077:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
vpos = strlen(tmp_cigar);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1118:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
next_char=fgetc(fp);
˜^˜˜˜˜˜˜˜˜
gene-algorithms.c:1123:15: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
next_char = get_next_char(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1165:84: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
ret += match_chro(read + last_section_end - min(0, section_offset), index, pos + last_section_end + max(0, section_offset), this_section_end - last_section_end + min(0, section_offset), is_negative_strand, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1165:110: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
ret += match_chro(read + last_section_end - min(0, section_offset), index, pos + last_section_end + max(0, section_offset), this_section_end - last_section_end + min(0, section_offset), is_negative_strand, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-algorithms.c:1267:30: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
anchor_read [anchors] = k;
˜ ^
gene-algorithms.c:1499:81: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_matched_base = gvindex_match_base(my_array_index, potential_position+i+bias, base_int);
˜^
gene-algorithms.c:1499:83: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int is_matched_base = gvindex_match_base(my_array_index, potential_position+i+bias, base_int);
˜^˜˜˜
gene-algorithms.c:1500:49: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
read_matchingness[bias+indel_tolerance][i] = is_matched_base;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1526:22: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
max_matchness = m*1.;
˜ ˜^˜˜
gene-algorithms.c:1631:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char is_matched_ij = gvindex_get(index, begin_position + path_j) == read[path_i]?DPALIGN_MATCH_SCORE :DPALIGN_MISMATCH_PENALTY;
˜ ^˜˜˜˜˜
gene-algorithms.c:1631:84: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char is_matched_ij = gvindex_get(index, begin_position + path_j) == read[path_i]?DPALIGN_MATCH_SCORE :DPALIGN_MISMATCH_PENALTY;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1631:105: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char is_matched_ij = gvindex_get(index, begin_position + path_j) == read[path_i]?DPALIGN_MATCH_SCORE :DPALIGN_MISMATCH_PENALTY;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1688:28: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
if (j==0) chro_str[i] = gvindex_get(index, begin_position+i);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1688:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (j==0) chro_str[i] = gvindex_get(index, begin_position+i);
˜^
gene-algorithms.c:1690:71: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read + i) == gvindex_get(index, begin_position + j + i) ;
˜ ^
gene-algorithms.c:1690:75: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read + i) == gvindex_get(index, begin_position + j + i) ;
˜ ^
gene-algorithms.c:1692:71: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read + i) == gvindex_get(index, begin_position - windows_number + j + 1 + i) ;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1692:88: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read + i) == gvindex_get(index, begin_position - windows_number + j + 1 + i) ;
˜ ^
gene-algorithms.c:1692:96: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read + i) == gvindex_get(index, begin_position - windows_number + j + 1 + i) ;
˜ ^
gene-algorithms.c:1703:93: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read - INDEL_WINDOW_WIDTH + i) == gvindex_get(index, begin_position + j + i - INDEL_WINDOW_WIDTH) ;
˜ ^
gene-algorithms.c:1703:97: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read - INDEL_WINDOW_WIDTH + i) == gvindex_get(index, begin_position + j + i - INDEL_WINDOW_WIDTH) ;
˜ ^
gene-algorithms.c:1705:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read - INDEL_WINDOW_WIDTH + i) == gvindex_get(index, begin_position -windows_number + j +1 + i - INDEL_WINDOW_WIDTH) ;
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1705:109: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read - INDEL_WINDOW_WIDTH + i) == gvindex_get(index, begin_position -windows_number + j +1 + i - INDEL_WINDOW_WIDTH) ;
˜ ^
gene-algorithms.c:1705:116: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
matchingness = *(read - INDEL_WINDOW_WIDTH + i) == gvindex_get(index, begin_position -windows_number + j +1 + i - INDEL_WINDOW_WIDTH) ;
˜ ^
gene-algorithms.c:1776:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
read[read_len] = j;
˜ ^
gene-algorithms.c:1813:40: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
if (i>0) from_upper = table[i-1][j] + (table_mask[i-1][j]?DPALIGN_EXTENDGAP_PENALTY:DPALIGN_CREATEGAP_PENALTY);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1814:26: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
else from_upper = DPALIGN_CREATEGAP_PENALTY;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1818:39: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
if (j>0) from_left = table[i][j-1] + (table_mask[i][j-1]?DPALIGN_EXTENDGAP_PENALTY:DPALIGN_CREATEGAP_PENALTY);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1819:25: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
else from_left = DPALIGN_CREATEGAP_PENALTY;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1821:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char chromo_ch = gvindex_get(index, begin_position + j);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1821:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char chromo_ch = gvindex_get(index, begin_position + j);
˜ ^
gene-algorithms.c:1822:48: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char is_matched_ij = (chromo_ch == read[i])?DPALIGN_MATCH_SCORE:DPALIGN_MISMATCH_PENALTY;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1822:68: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char is_matched_ij = (chromo_ch == read[i])?DPALIGN_MATCH_SCORE:DPALIGN_MISMATCH_PENALTY;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1849:25: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
short path_i = read_len-1 ;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜
gene-algorithms.c:1906:121: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_in_window = match_chro_wronglen(read+ window_end_pos - window_size, array_index, read_start_pos + window_end_pos - window_size, window_size, space_type, NULL, &right_match_number);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1906:138: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_in_window = match_chro_wronglen(read+ window_end_pos - window_size, array_index, read_start_pos + window_end_pos - window_size, window_size, space_type, NULL, &right_match_number);
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1935:40: warning: implicit conversion turns floating-point number into integer: 'float' to 'int' [-Wconversion]
int matched_bases_after_indel = match_chro_support(read +test_start, array_index, read_start_pos + indel_movement +test_start, test_length,0, space_type, qual_txt, qual_format);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1935:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_after_indel = match_chro_support(read +test_start, array_index, read_start_pos + indel_movement +test_start, test_length,0, space_type, qual_txt, qual_format);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1935:123: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_after_indel = match_chro_support(read +test_start, array_index, read_start_pos + indel_movement +test_start, test_length,0, space_type, qual_txt, qual_format);
˜^˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1950:27: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
*head_indel_pos = best_indel_pos;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1954:62: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
if(best_indel_pos<0) *head_indel_pos = window_end_pos - right_match_number;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1973:83: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int roughly_mapped = match_chro(read + cover_end, array_index, read_start_pos + cover_end + tail_indel, tail_test_len , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜
gene-algorithms.c:1973:95: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int roughly_mapped = match_chro(read + cover_end, array_index, read_start_pos + cover_end + tail_indel, tail_test_len , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1986:109: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_in_window = match_chro_wronglen(read+ window_start_pos, array_index, read_start_pos + window_start_pos + tail_indel, window_size, space_type, &left_match_number, NULL);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1986:128: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_in_window = match_chro_wronglen(read+ window_start_pos, array_index, read_start_pos + window_start_pos + tail_indel, window_size, space_type, &left_match_number, NULL);
˜ ^˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1994:107: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
roughly_mapped = match_chro(read+window_start_pos + left_match_number, array_index, read_start_pos + window_start_pos + tail_indel + left_match_number, read_len - window_start_pos - left_match_number , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1994:126: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
roughly_mapped = match_chro(read+window_start_pos + left_match_number, array_index, read_start_pos + window_start_pos + tail_indel + left_match_number, read_len - window_start_pos - left_match_number , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜
gene-algorithms.c:1994:139: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
roughly_mapped = match_chro(read+window_start_pos + left_match_number, array_index, read_start_pos + window_start_pos + tail_indel + left_match_number, read_len - window_start_pos - left_match_number , 0, space_type);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2015:40: warning: implicit conversion turns floating-point number into integer: 'float' to 'int' [-Wconversion]
int matched_bases_after_indel = match_chro_support(read + window_start_pos - min(0, indel_adjustment) + left_match_number, array_index, read_start_pos + window_start_pos + max(0,indel_movement) +left_match_number , test_length,0, space_type, qual_txt + window_start_pos - min(0, indel_adjustment) + left_match_number , qual_format);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2015:161: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_after_indel = match_chro_support(read + window_start_pos - min(0, indel_adjustment) + left_match_number, array_index, read_start_pos + window_start_pos + max(0,indel_movement) +left_match_number , test_length,0, space_type, qual_txt + window_start_pos - min(0, indel_adjustment) + left_match_number , qual_format);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2015:187: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_after_indel = match_chro_support(read + window_start_pos - min(0, indel_adjustment) + left_match_number, array_index, read_start_pos + window_start_pos + max(0,indel_movement) +left_match_number , test_length,0, space_type, qual_txt + window_start_pos - min(0, indel_adjustment) + left_match_number , qual_format);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-algorithms.c:2015:204: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_bases_after_indel = match_chro_support(read + window_start_pos - min(0, indel_adjustment) + left_match_number, array_index, read_start_pos + window_start_pos + max(0,indel_movement) +left_match_number , test_length,0, space_type, qual_txt + window_start_pos - min(0, indel_adjustment) + left_match_number , qual_format);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2032:44: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
*tail_indel_pos = window_start_pos + left_match_number ;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2034:26: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
*tail_indel_pos = best_indel_pos;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2059:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(pos < array_index -> start_base_offset || pos + read_len >= array_index -> start_base_offset + array_index -> length){
˜ ^˜˜˜˜˜˜˜
gene-algorithms.c:2066:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char true_chr = gvindex_get(array_index, pos + i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2066:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char true_chr = gvindex_get(array_index, pos + i);
˜ ^
gene-algorithms.c:2097:12: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return ret/1000000.;
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
gene-algorithms.c:2108:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(pos < array_index -> start_base_offset || pos + read_len >= array_index -> start_base_offset + array_index -> length){
˜ ^˜˜˜˜˜˜˜
gene-algorithms.c:2115:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char true_chr = gvindex_get(array_index, pos + i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2115:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char true_chr = gvindex_get(array_index, pos + i);
˜ ^
gene-algorithms.c:2156:12: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return ret/1000000.;
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
gene-algorithms.c:2218:41: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return max(1,(ret/10000.) / read_cursor+100.);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-algorithms.c:2169:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int cigar_length = strlen(cigar_txt);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2186:74: warning: implicit conversion loses integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]
float nret = match_base_quality(array_index, read_txt + read_cursor, chromosome_cursor , (qual_txt && qual_txt[0])?qual_txt + read_cursor:NULL, x, phred_version, mismatch);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2186:149: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
float nret = match_base_quality(array_index, read_txt + read_cursor, chromosome_cursor , (qual_txt && qual_txt[0])?qual_txt + read_cursor:NULL, x, phred_version, mismatch);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
gene-algorithms.c:2306:43: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return max(1., (ret/10000.) / read_cursor+100.);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-algorithms.c:2232:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int cigar_length = strlen(cigar_txt);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2249:79: warning: implicit conversion loses integer precision: 'long long' to 'unsigned int' [-Wshorten-64-to-32]
float nret = match_base_quality_edit(array_index, read_txt + read_cursor, chromosome_cursor , (qual_txt && qual_txt[0])?qual_txt + read_cursor:NULL, x, phred_version, mismatch);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2249:154: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
float nret = match_base_quality_edit(array_index, read_txt + read_cursor, chromosome_cursor , (qual_txt && qual_txt[0])?qual_txt + read_cursor:NULL, x, phred_version, mismatch);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
gene-algorithms.c:2335:49: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:63: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:77: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:91: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:105: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:119: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:133: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:147: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:161: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:175: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:189: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:203: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:217: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:231: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:245: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:259: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:273: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:287: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:301: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:315: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:329: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:343: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:357: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:371: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:385: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:399: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:413: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:427: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:441: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:455: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:469: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:483: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:497: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:511: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:525: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:539: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:553: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:567: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:581: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:595: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:609: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:623: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:637: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:651: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:665: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:679: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:693: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:707: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:721: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:735: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:749: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:763: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:777: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:791: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:805: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:819: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:833: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:847: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:861: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:875: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:889: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:903: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
˜ ^˜˜˜˜˜˜˜˜˜˜
gene-algorithms.c:2335:917: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
static float PROB_QUAL_TABLE[] = {1.000000000 , 0.794328235 , 0.630957344 , 0.501187234 , 0.398107171 , 0.316227766 , 0.251188643 , 0.199526231 , 0.158489319 , 0.125892541 , 0.100000000 , 0.079432823 , 0.063095734 , 0.050118723 , 0.039810717 , 0.031622777 , 0.025118864 , 0.019952623 , 0.015848932 , 0.012589254 , 0.010000000 , 0.007943282 , 0.006309573 , 0.005011872 , 0.003981072 , 0.003162278 , 0.002511886 , 0.001995262 , 0.001584893 , 0.001258925 , 0.001000000 , 0.000794328 , 0.000630957 , 0.000501187 , 0.000398107 , 0.000316228 , 0.000251189 , 0.000199526 , 0.000158489 , 0.000125893 , 0.000100000 , 0.000079433 , 0.000063096 , 0.000050119 , 0.000039811 , 0.000031623 , 0.000025119 , 0.000019953 , 0.000015849 , 0.000012589 , 0.000010000 , 0.000007943 , 0.000006310 , 0.000005012 , 0.000003981 , 0.000003162 , 0.000002512 , 0.000001995 , 0.000001585 , 0.000001259 , 0.000001000 , 0.000000794 , 0.000000631 , 0.000000501};
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189 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c gene-value-index.c -o gene-value-index.o
gene-value-index.c:59:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
unsigned char mask = 0x3 << (offset_bit);
˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:86:47: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
unsigned char mask = 0xff << (offset_bit+2) | 0xff >> (8-offset_bit);
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:121:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(&index->start_point,4,1, fp);
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gene-value-index.c:122:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(&index->length,4,1, fp);
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gene-value-index.c:138:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length =fread(index->values, 1, useful_bytes, fp);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:157:50: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_char = (pos <= index -> start_point)?'A': gvindex_get(index,pos-1);
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gene-value-index.c:161:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
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gene-value-index.c:161:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:201:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int npos = pos + i + max(0, offset);
˜ ^
gene-value-index.c:201:40: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int npos = pos + i + max(0, offset);
˜ ^˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-value-index.c:203:8: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
tt = gvindex_get (index, npos);
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gene-value-index.c:212:67: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int window_match = match_chro(read+i-min(0,offset), index, pos+i+ max(0, offset), INDEL_TEST_WINDOW ,0,GENE_SPACE_BASE);
˜^
gene-value-index.c:212:77: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int window_match = match_chro(read+i-min(0,offset), index, pos+i+ max(0, offset), INDEL_TEST_WINDOW ,0,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-value-index.c:225:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_tail = match_chro(read+i, index, pos+i+indel_test, test_len - i,0,GENE_SPACE_BASE);
˜^
gene-value-index.c:225:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_tail = match_chro(read+i, index, pos+i+indel_test, test_len - i,0,GENE_SPACE_BASE);
˜^˜˜˜˜˜˜˜˜˜
gene-value-index.c:234:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_tail = match_chro(read+i - indel_test, index, pos+i, test_len - i + indel_test ,0,GENE_SPACE_BASE);
˜^
gene-value-index.c:248:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
npos = pos + i + offset;
˜ ^
gene-value-index.c:248:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
npos = pos + i + offset;
˜ ^˜˜˜˜˜
gene-value-index.c:249:11: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
tt = gvindex_get (index, npos);
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gene-value-index.c:278:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(pos > 0xffff0000 || pos + test_len>= index-> length + index->start_point)
˜ ^˜˜˜˜˜˜˜
gene-value-index.c:286:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int npos = pos + i - max(0, offset);
˜ ^
gene-value-index.c:286:40: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int npos = pos + i - max(0, offset);
˜ ^˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-value-index.c:289:8: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
tt = gvindex_get (index, npos);
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gene-value-index.c:302:85: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int window_match = match_chro(read+i-min(0,offset)-INDEL_TEST_WINDOW, index, pos+i+ max(0, offset)-INDEL_TEST_WINDOW, INDEL_TEST_WINDOW ,0,GENE_SPACE_BASE);
˜^
gene-value-index.c:302:95: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int window_match = match_chro(read+i-min(0,offset)-INDEL_TEST_WINDOW, index, pos+i+ max(0, offset)-INDEL_TEST_WINDOW, INDEL_TEST_WINDOW ,0,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
gene-value-index.c:314:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_tail = match_chro(read , index, pos-indel_test, i ,0,GENE_SPACE_BASE);
˜^˜˜˜˜˜˜˜˜˜
gene-value-index.c:329:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int matched_tail = match_chro(read, index, pos - indel_test, i ,0,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜
gene-value-index.c:355:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
npos = (pos + i - offset);
˜ ^
gene-value-index.c:355:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
npos = (pos + i - offset);
˜ ^˜˜˜˜˜
gene-value-index.c:356:11: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
tt = gvindex_get (index, pos + i - offset);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:356:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tt = gvindex_get (index, pos + i - offset);
˜ ^
gene-value-index.c:356:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
tt = gvindex_get (index, pos + i - offset);
˜ ^˜˜˜˜˜
gene-value-index.c:383:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get(index, pos+test_len-1-i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:383:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get(index, pos+test_len-1-i);
˜^˜˜˜˜˜˜˜
gene-value-index.c:383:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get(index, pos+test_len-1-i);
˜^
gene-value-index.c:423:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:423:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:440:16: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:440:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:457:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:457:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:470:38: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return supported_qual*1. / all_qual * test_len;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
gene-value-index.c:484:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if ((unsigned int)(pos + test_len) >= index -> length + index -> start_point) return 0;
˜ ^˜˜˜˜˜˜˜
gene-value-index.c:493:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜^˜˜˜˜˜˜˜
gene-value-index.c:493:99: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜^˜˜˜˜˜˜˜
gene-value-index.c:493:77: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:496:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:496:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^˜˜˜˜˜˜˜
gene-value-index.c:496:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^
gene-value-index.c:506:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:506:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^˜˜˜˜˜˜˜
gene-value-index.c:506:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^
gene-value-index.c:529:21: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
char int_value = index->values [offset_byte];
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:555:18: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
int_value = index->values [offset_byte];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:562:51: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_char = (pos <= index -> start_point)?'A': gvindex_get(index,pos-1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:565:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:565:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:583:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int test_end = test_len+pos- index->start_base_offset;
^˜˜˜˜˜˜˜˜
gene-value-index.c:605:25: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
key[i] = key[i] << 2 | base2int(read[j]);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:617:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
search_dist = search_length /4;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
gene-value-index.c:631:50: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
test_offset += (search_to_back == SEARCH_BACK)?-i:i;
˜˜ ^˜
gene-value-index.c:631:53: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
test_offset += (search_to_back == SEARCH_BACK)?-i:i;
˜˜ ^
gene-value-index.c:640:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
hit_pos += index -> start_base_offset - j;// + index -> start_point;
˜ ^
gene-value-index.c:639:39: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
unsigned int hit_pos = test_offset*4;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
gene-value-index.c:666:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜^˜˜˜˜˜˜˜
gene-value-index.c:666:99: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜^˜˜˜˜˜˜˜
gene-value-index.c:666:77: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_char = (pos+test_len>= index -> length + index -> start_point)?'A': gvindex_get(index,pos+test_len);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:670:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:670:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^˜˜˜˜˜˜˜
gene-value-index.c:670:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos+test_len-1-i);
˜^
gene-value-index.c:690:51: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
last_char = (pos <= index -> start_point)?'A': gvindex_get(index,pos-1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:693:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char tt = gvindex_get (index, pos +i);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:693:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
char tt = gvindex_get (index, pos +i);
˜^
gene-value-index.c:717:27: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
unsigned char mask = 0x3 << (offset_bit);
˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:723:62: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
char reference_base = ((index->values [offset_byte] & mask) >> offset_bit);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:740:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
buf[i] = gvindex_get (index, pos + len - 1 - i);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:740:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
buf[i] = gvindex_get (index, pos + len - 1 - i);
˜ ^˜˜
gene-value-index.c:740:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
buf[i] = gvindex_get (index, pos + len - 1 - i);
˜ ^
gene-value-index.c:751:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
buf[i] = gvindex_get (index, pos +i);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gene-value-index.c:751:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
buf[i] = gvindex_get (index, pos +i);
˜^
80 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c hashtable.c -o hashtable.o
hashtable.c:65:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
malloc(numOfBuckets * sizeof(KeyValuePair *));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
hashtable.c:207:46: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:207:59: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:269:51: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:269:64: warning: implicit conversion changes signedness: 'const long' to 'unsigned long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:296:51: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:296:64: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(key) % hashTable->numOfBuckets;
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:539:40: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
malloc(numOfBuckets * sizeof(KeyValuePair *));
^˜˜˜˜˜˜˜˜˜˜˜ ˜
hashtable.c:553:65: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(pair->key) % numOfBuckets;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:553:67: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
long hashValue = hashTable->hashFunction(pair->key) % numOfBuckets;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
hashtable.c:699:55: warning: implicit conversion turns floating-point number into integer: 'float' to 'long' [-Wconversion]
long idealNumOfBuckets = hashTable->numOfElements / hashTable->idealRatio;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c index-builder.c -o index-builder.o
index-builder.c:33:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
for(i=strlen(outbuff); i<105; i++)
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:45:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int segment_size = (int)(memory_megabytes * 1024.0 / 9.15) * 1024 ;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
index-builder.c:193:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = geinput_next_char(&ginp);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:203:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int_key = genekey2color('A',window);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:205:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = genekey2int(window,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:210:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = int_key = genekey2int(window,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:222:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
offset -= seek_back_reads;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:230:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
offset -= seek_back_reads;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:256:18: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char bnch = fgetc(ginp.input_fp);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:262:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = geinput_next_char(&ginp);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:270:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int_key = genekey2color('A',window);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:272:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = genekey2int(window,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:277:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = int_key = genekey2int(window, GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:309:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
next_char = geinput_next_char(&ginp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:330:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int_key += chars2color(last_color_base, next_char);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:353:58: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
print_build_log(finished_rate,base_per_second,ETA, all_bases);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
index-builder.c:387:102: warning: implicit conversion loses integer precision: 'unsigned int' to 'unsigned char' [-Wconversion]
huge_index[ (huge_byte >> 20) & 1023 ][huge_byte&0xfffff] = (byte_value & (˜(0x3 << huge_offset))) | (huge_value << huge_offset);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:387:78: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
huge_index[ (huge_byte >> 20) & 1023 ][huge_byte&0xfffff] = (byte_value & (˜(0x3 << huge_offset))) | (huge_value << huge_offset);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:387:116: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
huge_index[ (huge_byte >> 20) & 1023 ][huge_byte&0xfffff] = (byte_value & (˜(0x3 << huge_offset))) | (huge_value << huge_offset);
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:391:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int matched = gehash_get(tab, subr, ×, 1);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:408:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float local_begin_ftime = miltime();
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
index-builder.c:498:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = geinput_next_char(&ginp);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:509:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int_key = genekey2color('A',window);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:511:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = genekey2int(window,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:516:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
array_int_key = int_key = genekey2int(window,GENE_SPACE_BASE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:532:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
next_char = geinput_next_char(&ginp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:553:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int_key += chars2color(last_color_base, next_char);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:580:58: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
print_build_log(finished_rate,base_per_second,ETA, all_bases);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
index-builder.c:640:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
while ((c = getopt (argc, argv, "cqM:o:f:D?")) != -1)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
index-builder.c:686:65: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(build_gene_index(output_file, argv+optind , argc - optind, memory_limit, threshold, &huge_table)) return 1;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
30 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c input-files.c -o input-files.o
input-files.c:93:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char ch = fgetc(fp);
˜˜ ^˜˜˜˜˜˜˜˜
input-files.c:96:19: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
buff[ret++] = toupper(ch);
˜ ^˜˜˜˜˜˜˜˜˜˜
input-files.c:103:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char ch = fgetc(fp);
˜˜ ^˜˜˜˜˜˜˜˜
input-files.c:123:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char ch = fgetc(fp);
˜˜ ^˜˜˜˜˜˜˜˜
input-files.c:134:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
buff[ret++] = toupper(ch);
˜ ^˜˜˜˜˜˜˜˜˜˜
input-files.c:141:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char ch = fgetc(fp);
˜˜ ^˜˜˜˜˜˜˜˜
input-files.c:277:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char nch = fgetc(input->input_fp);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:332:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:337:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = fgetc(input->input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:339:5: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:343:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:349:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:350:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:354:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:355:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:356:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:357:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:370:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = fgetc(input->input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:372:5: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:379:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:449:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chro_pos = chro_pos*10+(in_buff[i]-'0');
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜
input-files.c:575:11: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = fgetc(input->input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:599:4: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE;
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:604:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = fgetc(input->input_fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:631:3: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE;
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:637:4: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
SKIP_LINE;
^˜˜˜˜˜˜˜˜
input-files.c:326:69: note: expanded from macro 'SKIP_LINE'
#define SKIP_LINE { nch=' '; while(nch != EOF && nch != '\n') nch = fgetc(input->input_fp); }
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:802:77: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float step = max(3.00001, (len-16-GENE_SLIDING_STEP)*1.0/(TOTAL_SUBREADS-1)+0.00001);
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./subread.h:315:29: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
input-files.c:802:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float step = max(3.00001, (len-16-GENE_SLIDING_STEP)*1.0/(TOTAL_SUBREADS-1)+0.00001);
˜˜˜˜ ^˜˜˜˜˜˜
./subread.h:315:33: note: expanded from macro 'max'
#define max(a,b) ((a)<(b)?(b):(a))
^
input-files.c:847:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
ret_pos = ret_pos * 10 + (cc-'0');
˜ ˜˜^˜˜˜
input-files.c:888:58: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(max_base_position)*max_base_position=min((block_no+1)*BASE_BLOCK_LENGTH, max_known_chromosome);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./subread.h:316:33: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
input-files.c:879:54: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
max_known_chromosome = known_chromosomes[chro_no].known_length;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
input-files.c:934:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(sequence , 1, rl,temp_fp );
˜˜˜˜˜˜ ^˜
input-files.c:935:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(quality_string , 1, rl,temp_fp );
˜˜˜˜˜˜ ^˜
input-files.c:991:104: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
known_chromosomes[chro_numb].known_length = known_chromosomes[chro_numb].known_length * 10 + (cc - '0');
˜ ˜˜˜^˜˜˜˜
input-files.c:1038:54: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
while(insertion_cursor < (chromosome_cursor + tmpv) && read_cursor < (rl - base_ignored_head_tail))
˜ ^˜˜˜
input-files.c:1044:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insert_length = min(max_section_pos + 1, chromosome_cursor + tmpv) - insertion_cursor;
˜ ^˜˜˜
./subread.h:316:25: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
input-files.c:1044:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insert_length = min(max_section_pos + 1, chromosome_cursor + tmpv) - insertion_cursor;
˜ ^˜˜˜
./subread.h:316:29: note: expanded from macro 'min'
#define min(a,b) ((a)>(b)?(b):(a))
^
input-files.c:1049:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(read_cursor+insert_length < base_ignored_head_tail)
^˜˜˜˜˜˜˜˜˜˜˜
input-files.c:1054:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insert_length = read_cursor + insert_length - base_ignored_head_tail;
^˜˜˜˜˜˜˜˜˜˜ ˜
input-files.c:1054:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insert_length = read_cursor + insert_length - base_ignored_head_tail;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:1057:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insertion_cursor += ignored_length;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:1062:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
else if(read_cursor +insert_length >= (rl - base_ignored_head_tail))
^˜˜˜˜˜˜˜˜˜˜ ˜
input-files.c:1063:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
insert_length = (rl - base_ignored_head_tail) - read_cursor;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:1071:176: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
write_read_block_file(temp_fp , read_number, read_name, flags, chro, insertion_cursor, cigar, mapping_quality, sequence + read_cursor , quality_string + read_cursor, insert_length , 1, is_negative_strand);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
input-files.c:1081:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chromosome_cursor += tmpv;
˜˜ ^˜˜˜
input-files.c:1087:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chromosome_cursor += tmpv;
˜˜ ^˜˜˜
input-files.c:1208:40: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
exon_location = exon_location*10 + buff[i] - '0';
˜ ^˜˜˜˜˜˜
input-files.c:1221:40: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
exon_location = exon_location*10 + buff[i] - '0';
˜ ^˜˜˜˜˜˜
48 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c processExons.c -o processExons.o
processExons.c:216:10: warning: unused variable 'pt' [-Wunused-variable]
char *pt = strcpy(gene_array[gene_pos].chr_array[current_chr_index].id,chr_id);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c propmapped.c -o propmapped.o
propmapped.c:27:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
propmapped.c:21:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
propmapped.c:20:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
propmapped.c:49:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c qualityScores.c -o qualityScores.o
qualityScores.c:52:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
qualityScores.c:11:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
qualityScores.c:12:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
qualityScores.c:17:7: warning: unused variable 'data_ready' [-Wunused-variable]
int data_ready=1;
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c readSummary.c -o readSummary.o
In file included from readSummary.c:7:
./sambam-file.h:50:2: warning: anonymous unions are a C11 extension [-Wc11-extensions]
union{
^
readSummary.c:62:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readSummary.c:81:25: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
geneid = (int *) calloc(nexons,sizeof(int));
˜˜˜˜˜˜ ^˜˜˜˜˜
readSummary.c:82:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
chr = (char **) calloc(nexons,sizeof(char *));
˜˜˜˜˜˜ ^˜˜˜˜˜
readSummary.c:83:25: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
start = (long *) calloc(nexons,sizeof(long));
˜˜˜˜˜˜ ^˜˜˜˜˜
readSummary.c:84:24: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
stop = (long *) calloc(nexons,sizeof(long));
˜˜˜˜˜˜ ^˜˜˜˜˜
readSummary.c:85:25: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
nreads = (int *) calloc(nexons,sizeof(int));
˜˜˜˜˜˜ ^˜˜˜˜˜
readSummary.c:111:62: warning: use of non-standard escape character '\%' [-Wpedantic]
Rprintf("Number of chromosomes included in the annotation is \%d\n",nchr);
^˜
readSummary.c:38:9: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
readSummary.c:37:8: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
readSummary.c:107:8: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
nchr = curchr;
˜ ^˜˜˜˜˜
readSummary.c:140:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = strlen(strtok(NULL,"\t"));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readSummary.c:217:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
pos_leftmost = read_pos;
˜ ^˜˜˜˜˜˜˜
readSummary.c:275:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c removeDupReads.c -o removeDupReads.o
removeDupReads.c:53:54: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int block_start_base = BASE_BLOCK_LENGTH * i;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
removeDupReads.c:46:82: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int block_in_chro = chromosomes[chromosome_no].known_length / BASE_BLOCK_LENGTH+1;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
removeDupReads.c:114:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(line_buffer, linelen, 1, out_fp);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
removeDupReads.c:125:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if(is_read_selected(read_selection_list, read_no)){
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
removeDupReads.c:126:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(line_buffer, linelen, 1, out_fp);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
removeDupReads.c:232:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
while ((c = getopt (argc, argv, "i:o:r:t:c:?")) != -1)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
removeDupReads.c:259:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
read_count = atoi(optarg);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sam2bed.c -o sam2bed.o
sam2bed.c:31:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
line = (char*)calloc(MAX_LINE_LENGTH, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sam2bed.c:23:11: warning: unused variable 'z' [-Wunused-variable]
ssize_t z;
^
sam2bed.c:22:10: warning: unused variable 'len' [-Wunused-variable]
size_t len = 0;
^
sam2bed.c:52:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:7:
./sambam-file.h:50:2: warning: anonymous unions are a C11 extension [-Wc11-extensions]
union{
^
sambam-file.c:54:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
unsigned char first_ch = fgetc(os_file);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:55:29: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
unsigned char second_ch = fgetc(os_file);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:82:63: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
ret -> bam_file_next_section_start = gztell(ret -> gz_file) + l_text;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
sambam-file.c:102:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
unsigned long long head_pos = gztell(fp->gz_file);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:138:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gzread(fp->gz_file, aln -> read_name, read_name_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:157:48: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int seq_qual_bytes = read_len + (read_len /2)+(read_len%2);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:158:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int gzread_len = gzread(fp->gz_file, aln-> buff_for_seq, seq_qual_bytes);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:177:66: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
read_2_seq = aln -> buff_for_seq[(read_len /2)+(read_len%2) + xk1] ;
˜ ^˜˜
sambam-file.c:183:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
unsigned long long tail_pos = gztell(fp->gz_file);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:187:47: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
long long int seek_ret= gzseek(fp->gz_file, skip_len, SEEK_CUR);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
sambam-file.c:222:22: warning: implicit conversion changes signedness: 'BS_uint_32' (aka 'unsigned int') to 'int' [-Wsign-conversion]
int ref_name_len = gzread_B32(ret -> gz_file);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:226:65: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
gzread(ret -> gz_file, ret -> bam_chro_table[xk1].chro_name , ref_readin_len);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:238:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
ret ->bam_chro_table_size = ref_info_size;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:261:11: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
nch = gzgetc(fp->gz_file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sambam-file.c:336:11: warning: unused variable 'buf2' [-Wunused-variable]
char * buf2 = SamBam_fgets(fp,buf, 3000);
^
16 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c:48:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
expected_bucket_number *
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
sorted-hashtable.c:25:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
expected_bucket_number = expected_size / GEHASH_BUCKET_LENGTH;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:82:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_item_keys = (gehash_key_t *) malloc(sizeof(gehash_key_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:83:70: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_item_values = (gehash_data_t *) malloc(sizeof(gehash_data_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:91:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(new_item_keys, sizeof(gehash_key_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:92:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(new_item_values, sizeof(gehash_data_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:166:67: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_item_keys = (gehash_key_t *) malloc(sizeof(gehash_key_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:167:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
new_item_values = (gehash_data_t *) malloc(sizeof(gehash_data_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:176:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(new_item_keys, sizeof(gehash_key_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:177:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(new_item_values, sizeof(gehash_data_t) * new_bucket_length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:179:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_item_keys, current_bucket->item_keys, current_bucket->current_items*sizeof(gehash_key_t));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sorted-hashtable.c:179:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_item_keys, current_bucket->item_keys, current_bucket->current_items*sizeof(gehash_key_t));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sorted-hashtable.c:180:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_item_values, current_bucket->item_values, current_bucket->current_items*sizeof(gehash_data_t));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
sorted-hashtable.c:180:73: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(new_item_values, current_bucket->item_values, current_bucket->current_items*sizeof(gehash_data_t));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
sorted-hashtable.c:199:36: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
bucket_number = _gehash_hash(key) % the_table -> buckets_number;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:199:51: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bucket_number = _gehash_hash(key) % the_table -> buckets_number;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:213:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
bucket_number = _gehash_hash(key) % the_table -> buckets_number;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:213:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bucket_number = _gehash_hash(key) % the_table -> buckets_number;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:247:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
error_pos_stack [i] = i;
˜ ^
sorted-hashtable.c:266:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mutation_key = mutation_key & ˜(0x3 << (2*base_to_change));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:267:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mutation_key = mutation_key | (new_value << (2*base_to_change));
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:287:47: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
error_pos_stack[j] = error_pos_stack[i] + (j-i);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
sorted-hashtable.c:295:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return ret;
˜˜˜˜˜˜ ^˜˜
sorted-hashtable.c:347:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mutation_key = mutation_key & ˜(0x3 << (2*(15-base_to_change)));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:348:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mutation_key = mutation_key | (new_value << (2*(15-base_to_change)));
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:377:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return ret;
˜˜˜˜˜˜ ^˜˜
sorted-hashtable.c:437:55: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
short offset_from_5 = is_reversed?(read_len - offset - 16):offset ;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
sorted-hashtable.c:437:61: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
short offset_from_5 = is_reversed?(read_len - offset - 16):offset ;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
sorted-hashtable.c:443:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
unsigned int kv = (*keyp) - offset;
˜ ^˜˜˜˜˜
sorted-hashtable.c:526:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
kv -= offset;
˜˜ ^˜˜˜˜˜
sorted-hashtable.c:530:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int offsetX = _index_vote_tol(kv+iix);
˜^˜˜
sorted-hashtable.c:229:47: note: expanded from macro '_index_vote_tol'
#define _index_vote_tol(key) (((unsigned int)(key)/INDEL_SEGMENT_SIZE)%GENE_VOTE_TABLE_SIZE)
^
sorted-hashtable.c:538:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int di = dat[i];
˜˜ ^˜˜˜˜˜
sorted-hashtable.c:539:20: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int dist0 = kv-di;
˜˜˜˜˜ ˜˜^˜˜
sorted-hashtable.c:539:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int dist0 = kv-di;
˜^˜
sorted-hashtable.c:550:39: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
vote -> last_offset[offsetX][i]=offset;
˜^˜˜˜˜˜
sorted-hashtable.c:575:66: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
vote -> indel_recorder[offsetX][i][toli] = subread_number+1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
sorted-hashtable.c:576:54: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
vote -> indel_recorder[offsetX][i][toli+2] = dist0;
˜ ^˜˜˜˜
sorted-hashtable.c:582:66: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
vote -> indel_recorder[offsetX][i][toli+1] = subread_number+1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
sorted-hashtable.c:609:29: warning: implicit conversion changes signedness: 'int' to 'gehash_data_t' (aka 'unsigned int') [-Wsign-conversion]
vote->max_position = di;
˜ ^˜
sorted-hashtable.c:635:46: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
vote -> last_offset[offsetX2][datalen2]=offset;
˜^˜˜˜˜˜
sorted-hashtable.c:641:68: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
vote -> indel_recorder[offsetX2][datalen2][0] = subread_number+1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
sorted-hashtable.c:642:68: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
vote -> indel_recorder[offsetX2][datalen2][1] = subread_number+1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
sorted-hashtable.c:428:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
match_start = keyp - current_bucket -> item_keys;
˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:433:19: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
match_end = keyp - current_bucket -> item_keys;
˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:803:38: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
while(current_bucket -> item_keys [i+removed] == key && i+removed < current_bucket -> current_items)
^˜
sorted-hashtable.c:803:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
while(current_bucket -> item_keys [i+removed] == key && i+removed < current_bucket -> current_items)
^˜
sorted-hashtable.c:806:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if(i+removed >= current_bucket -> current_items)
^˜
sorted-hashtable.c:812:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
current_bucket -> item_keys [i + removed];
^ ˜
sorted-hashtable.c:815:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
current_bucket -> item_values [i + removed];
^ ˜
sorted-hashtable.c:828:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return -1;
˜˜˜˜˜˜ ^˜
sorted-hashtable.c:860:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return ret;
˜˜˜˜˜˜ ^˜˜
sorted-hashtable.c:858:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(&ret, sizeof(int), 1, fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:867:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(&ret, sizeof(long long int), 1, fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:886:31: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
the_table -> current_items = load_int64(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:887:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
the_table -> buckets_number = load_int32(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:888:101: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
the_table -> buckets = (struct gehash_bucket * )malloc(sizeof(struct gehash_bucket) * the_table -> buckets_number);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:898:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
current_bucket -> current_items = load_int32(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:899:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
current_bucket -> space_size = load_int32(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:901:100: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
current_bucket -> item_keys = (gehash_key_t *) malloc ( sizeof(gehash_key_t) * current_bucket -> space_size);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:902:104: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
current_bucket -> item_values = (gehash_data_t *) malloc ( sizeof(gehash_data_t) * current_bucket -> space_size);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:913:93: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
read_length = fread(current_bucket -> item_keys, sizeof(gehash_key_t), current_bucket -> current_items, fp);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:915:96: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
read_length = fread(current_bucket -> item_values, sizeof(gehash_data_t), current_bucket -> current_items, fp);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:913:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(current_bucket -> item_keys, sizeof(gehash_key_t), current_bucket -> current_items, fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:915:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(current_bucket -> item_values, sizeof(gehash_data_t), current_bucket -> current_items, fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:921:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
read_length = fread(&(the_table -> is_small_table), sizeof(char), 1, fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:950:50: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
print_text_scrolling_bar("Saving index", 1.0*i/the_table -> buckets_number, 80, &scroll_counter);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:975:79: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(current_bucket -> item_keys, sizeof(gehash_key_t), current_bucket -> current_items, fp);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sorted-hashtable.c:976:82: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(current_bucket -> item_values, sizeof(gehash_data_t), current_bucket -> current_items, fp);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
68 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rsubread.so R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)