R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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> if (.Platform$OS.type != "windows")
+ BiocGenerics:::testPackage("SeqArray")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
The following object is masked from 'package:SeqArray':
rowRanges
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:SeqArray':
rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeqArray':
colData
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Running the examples in 'KG_P1_SampData()':
Running the examples in 'SeqArray-package()':
Tue Apr 9 03:36:04 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:04 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.5K)
# of fragments: 159
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:04 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99
Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62
Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54
Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
<None>
# of selected samples: 5
# of selected variants: 10
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs3762001"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs73134914"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs115805274"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs34424078"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs16940094"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs114467444"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs75372730"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs72483216"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs112301322"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs11554369"
# of selected samples: 90
# of selected variants: 1,348
Running the examples in 'SeqVarGDSClass()':
Running the examples in 'seqAlleleFreq()':
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Running the examples in 'seqApply()':
# of selected samples: 5
# of selected variants: 10
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 01 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 01
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 01 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 01 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 1 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 1 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 01 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 01 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 01 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 01 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs3762001"
$DP
index
sample [,1]
[1,] 16
[2,] 64
[3,] 61
[4,] 84
[5,] 89
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs73134914"
$DP
index
sample [,1]
[1,] 4
[2,] 2
[3,] 9
[4,] 60
[5,] 159
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs115805274"
$DP
index
sample [,1]
[1,] 27
[2,] 111
[3,] 42
[4,] 96
[5,] 153
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs34424078"
$DP
index
sample [,1]
[1,] 13
[2,] 34
[3,] 23
[4,] 53
[5,] 141
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs16940094"
$DP
index
sample [,1]
[1,] 43
[2,] 62
[3,] 50
[4,] 52
[5,] 127
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs114467444"
$DP
index
sample [,1]
[1,] 13
[2,] 7
[3,] 11
[4,] 28
[5,] 50
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs75372730"
$DP
index
sample [,1]
[1,] 2
[2,] 15
[3,] 38
[4,] 18
[5,] 63
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs72483216"
$DP
index
sample [,1]
[1,] 13
[2,] 105
[3,] 45
[4,] 78
[5,] 70
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs112301322"
$DP
index
sample [,1]
[1,] 12
[2,] 59
[3,] 66
[4,] 84
[5,] 77
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs11554369"
$DP
index
sample [,1]
[1,] 8
[2,] 31
[3,] 54
[4,] 41
[5,] 46
1
0
0
1
1
1
0
0
0
0
[1] 1
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs3762001"
[1] 2
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs73134914"
[1] 3
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs115805274"
[1] 4
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs34424078"
[1] 5
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs16940094"
[1] 6
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs114467444"
[1] 7
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs75372730"
[1] 8
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs72483216"
[1] 9
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs112301322"
[1] 10
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$rsid
[1] "rs11554369"
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 1 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 1 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
$sample.id
[1] "NA06985"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
$sample.id
[1] "NA06989"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
$sample.id
[1] "NA07000"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
$sample.id
[1] "NA07048"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 1 0 0 0 0
$sample.id
[1] "NA07346"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 1 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
Running the examples in 'seqAsVCF()':
Running the examples in 'seqBED2GDS()':
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Tue Apr 9 03:36:04 2019
PLINK BED to SeqArray GDS Format:
BED file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz' in the SNP-major mode (Sample X SNP)
FAM file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz' (60 samples)
BIM file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz' (5,000 variants)
sample.id [md5: b74526f3626e38cb16ca0f430e14a5ec]
variant.id [md5: 46b9b8513fddb695e351385ee3c6f177]
position [md5: 5ce9fe5d7fb8ed55cf8518b777951219]
chromosome [md5: 1e7c9ebb547f153137f8840b56220bf5]
allele [md5: 8ac94702b318deb38950aec11c50fb60]
genotype [md5: a4c1462aa0dbbf2333ef09a5fb02e67d]
phase [md5: 982a3a9e10be5cb4326775709384ee33]
annotation/id [md5: 2ffacef2573cdad31273b89903287925]
annotation/qual [md5: 0246b3fc665ce36bb8882d5d73bb7b4c]
annotation/filter [md5: e06fa4c84d9e6d743ee16d4e64ddacac]
sample.annotation
Done.
Tue Apr 9 03:36:05 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (80.5K)
# of fragments: 104
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (79.8K, reduced: 672B)
# of fragments: 48
Tue Apr 9 03:36:05 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: unknown
Ploidy: 2
Number of samples: 60
Number of variants: 5,000
Chromosomes:
Chr1 : 365, Chr2 : 417, Chr3 : 339, Chr4 : 307, Chr5 : 313, Chr6 : 357
Chr7 : 236, Chr8 : 249, Chr9 : 223, Chr10: 267, Chr11: 277, Chr12: 228
Chr13: 185, Chr14: 141, Chr15: 156, Chr16: 150, Chr17: 108, Chr18: 143
Chr19: 89 , Chr20: 117, Chr21: 69 , Chr22: 61 , Chr23: 203
Alleles:
ALT: <None>
tabulation: 2, 5000(100.0%)
Annotation, Quality:
Min: 100, 1st Qu: 100, Median: 100, Mean: 100, 3rd Qu: 100, Max: 100
Annotation, FILTER:
PASS, All filters passed, 5000(100.0%)
Annotation, INFO variable(s):
<None>
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
Annotation, sample variable(s):
family, Integer, <NA>
father, Integer, <NA>
mother, Integer, <NA>
sex, String, <NA>
phenotype, Integer, <NA>
Running the examples in 'seqBlockApply()':
# of selected samples: 5
# of selected variants: 10
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 1
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 1 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 1 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 0 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 01 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 01
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 01 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 01 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 1 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 1 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 01 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 01 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 00 00 00 00
[2,] 00 00 00 00 00 01 00 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 01 00 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 00 00 00
variant
sample [,1] [,2] [,3]
[1,] 1 2 2
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
variant
sample [,1] [,2] [,3]
[1,] 2 2 2
[2,] 2 1 2
[3,] 2 2 2
[4,] 2 2 1
[5,] 1 2 2
variant
sample [,1] [,2] [,3]
[1,] 2 2 2
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
variant
sample [,1]
[1,] 2
[2,] 2
[3,] 2
[4,] 2
[5,] 2
$dos
variant
sample [,1] [,2] [,3]
[1,] 1 2 2
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
$pos
[1] 143864805 72487157 80328908
$dos
variant
sample [,1] [,2] [,3]
[1,] 2 2 2
[2,] 2 1 2
[3,] 2 2 2
[4,] 2 2 1
[5,] 1 2 2
$pos
[1] 90751641 23316941 45492190
$dos
variant
sample [,1] [,2] [,3]
[1,] 2 2 2
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
$pos
[1] 3363976 30796109 35198045
$dos
variant
sample [,1]
[1,] 2
[2,] 2
[3,] 2
[4,] 2
[5,] 2
$pos
[1] 52444656
Running the examples in 'seqCheck()':
Open '/home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds'
Hash check:
sample.id: 'md5' [OK]
variant.id: 'md5' [OK]
position: 'md5' [OK]
chromosome: 'md5' [OK]
allele: 'md5' [OK]
genotype/data: 'md5' [OK]
genotype/@data: 'md5' [OK]
phase/data: 'md5' [OK]
annotation/id: 'md5' [OK]
annotation/qual: 'md5' [OK]
annotation/filter: 'md5' [OK]
annotation/info/AA: 'md5' [OK]
annotation/info/@AA: 'md5' [OK]
annotation/info/AC: 'md5' [OK]
annotation/info/AN: 'md5' [OK]
annotation/info/DP: 'md5' [OK]
annotation/info/HM2: 'md5' [OK]
annotation/info/HM3: 'md5' [OK]
annotation/info/OR: 'md5' [OK]
annotation/info/GP: 'md5' [OK]
annotation/info/BN: 'md5' [OK]
annotation/format/DP/data: 'md5' [OK]
annotation/format/DP/@data: 'md5' [OK]
Dimension check:
variant.id [OK]
position [OK]
chromosome [OK]
allele [OK]
annotation/id [OK]
annotation/qual [OK]
annotation/filter [OK]
annotation/info/AA [OK]
annotation/info/AC [OK]
annotation/info/AN [OK]
annotation/info/DP [OK]
annotation/info/HM2 [OK]
annotation/info/HM3 [OK]
annotation/info/OR [OK]
annotation/info/GP [OK]
annotation/info/BN [OK]
Running the examples in 'seqClose-methods()':
Running the examples in 'seqDelete()':
Delete INFO variable(s): HM2 AA
Delete FORMAT variable(s): DP
Delete Sample Annotation variable(s):
Clean up the fragments of GDS file:
open the file 'tmp.gds' (299.1K)
# of fragments: 77
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (63.3K, reduced: 235.7K)
# of fragments: 64
Running the examples in 'seqDigest()':
Running the examples in 'seqExampleFileName()':
Running the examples in 'seqExport()':
# of selected samples: 8
# of selected variants: 100
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 5260e8825b753db5240e1adc3208fae4]
position [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
chromosome [md5: 31101f0b9c3a15be71aa9904b49776e0]
allele [md5: 7b70b62ea10c297f4b44411c0247a346]
genotype [md5: 418d339cc0bad5eed558e6555970240b]
[md5: 9af8a70f41fa6c1822aff9ec427e78bf]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: 43e4c471f036cf267d9ad898c9a4d552]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: e8070827ea4aa58a1b22a6a0bbd04238]
annotation/info/AC [md5: 3683b41616fc897f3806db6c665eead2]
annotation/info/AN [md5: 2cbdb642a0402ace8a15642bad729454]
annotation/info/DP [md5: 3e41693488201ee0913f044ddff0b352]
annotation/info/HM2 [md5: 9bdbd7c2223bca753a035e717be81c4b]
annotation/info/HM3 [md5: 4c7060bd7024bc44392519fe36a927f9]
annotation/info/OR [md5: f82ffa7301b6d86fa158e0547a9d8823]
annotation/info/GP [md5: 86ccad572dbf631507a84ef6a586ba78]
annotation/info/BN [md5: 026894e1ea6f5f60c3faa919ad75a233]
annotation/format/DP [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
[md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (17.8K)
# of fragments: 149
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (17.0K, reduced: 864B)
# of fragments: 77
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 5260e8825b753db5240e1adc3208fae4]
position [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
chromosome [md5: 31101f0b9c3a15be71aa9904b49776e0]
allele [md5: 7b70b62ea10c297f4b44411c0247a346]
genotype [md5: 418d339cc0bad5eed558e6555970240b]
[md5: 9af8a70f41fa6c1822aff9ec427e78bf]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: 43e4c471f036cf267d9ad898c9a4d552]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/format/DP [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
[md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (12.5K)
# of fragments: 107
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (11.9K, reduced: 600B)
# of fragments: 57
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 5260e8825b753db5240e1adc3208fae4]
position [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
chromosome [md5: 31101f0b9c3a15be71aa9904b49776e0]
allele [md5: 7b70b62ea10c297f4b44411c0247a346]
genotype [md5: 418d339cc0bad5eed558e6555970240b]
[md5: 9af8a70f41fa6c1822aff9ec427e78bf]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: 43e4c471f036cf267d9ad898c9a4d552]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: e8070827ea4aa58a1b22a6a0bbd04238]
annotation/info/AC [md5: 3683b41616fc897f3806db6c665eead2]
annotation/info/AN [md5: 2cbdb642a0402ace8a15642bad729454]
annotation/info/DP [md5: 3e41693488201ee0913f044ddff0b352]
annotation/info/HM2 [md5: 9bdbd7c2223bca753a035e717be81c4b]
annotation/info/HM3 [md5: 4c7060bd7024bc44392519fe36a927f9]
annotation/info/OR [md5: f82ffa7301b6d86fa158e0547a9d8823]
annotation/info/GP [md5: 86ccad572dbf631507a84ef6a586ba78]
annotation/info/BN [md5: 026894e1ea6f5f60c3faa919ad75a233]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (14.7K)
# of fragments: 133
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (14.0K, reduced: 756B)
# of fragments: 70
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 5260e8825b753db5240e1adc3208fae4]
position [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
chromosome [md5: 31101f0b9c3a15be71aa9904b49776e0]
allele [md5: 7b70b62ea10c297f4b44411c0247a346]
genotype [md5: 418d339cc0bad5eed558e6555970240b]
[md5: 9af8a70f41fa6c1822aff9ec427e78bf]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: 43e4c471f036cf267d9ad898c9a4d552]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: e8070827ea4aa58a1b22a6a0bbd04238]
annotation/info/AC [md5: 3683b41616fc897f3806db6c665eead2]
annotation/info/AN [md5: 2cbdb642a0402ace8a15642bad729454]
annotation/info/DP [md5: 3e41693488201ee0913f044ddff0b352]
annotation/info/HM2 [md5: 9bdbd7c2223bca753a035e717be81c4b]
annotation/info/HM3 [md5: 4c7060bd7024bc44392519fe36a927f9]
annotation/info/OR [md5: f82ffa7301b6d86fa158e0547a9d8823]
annotation/info/GP [md5: 86ccad572dbf631507a84ef6a586ba78]
annotation/info/BN [md5: 026894e1ea6f5f60c3faa919ad75a233]
annotation/format/DP [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
[md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (17.4K)
# of fragments: 144
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (16.6K, reduced: 828B)
# of fragments: 75
Running the examples in 'seqGDS2SNP()':
Tue Apr 9 03:36:06 2019
SeqArray GDS to SNP GDS Format:
# of samples: 90
# of variants: 1,348
genotype compression: LZMA_RA
annotation compression: LZMA_RA
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Done.
Tue Apr 9 03:36:06 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (26.5K)
# of fragments: 31
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (26.3K, reduced: 192B)
# of fragments: 15
Tue Apr 9 03:36:06 2019
Running the examples in 'seqGDS2VCF()':
# of selected samples: 5
Tue Apr 9 03:36:06 2019
VCF Export: tmp.vcf.gz
5 samples, 1,348 variants
INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
FORMAT Field: DP
output to BGZF format
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Tue Apr 9 03:36:06 2019 Done.
Tue Apr 9 03:36:06 2019
VCF Export: tmp1.vcf.gz
5 samples, 1,348 variants
INFO Field: <none>
FORMAT Field: <none>
output to BGZF format
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Tue Apr 9 03:36:06 2019 Done.
Tue Apr 9 03:36:06 2019
VCF Export: tmp2.vcf.gz
5 samples, 1,348 variants
INFO Field: BN, GP, AA, DP, HM2
FORMAT Field: <none>
output to BGZF format
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Tue Apr 9 03:36:06 2019 Done.
# of selected samples: 90
# of selected variants: 1,348
Tue Apr 9 03:36:06 2019
VCF Export: tmp.vcf.gz
90 samples, 1,348 variants
INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
FORMAT Field: DP
output to BGZF format
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Tue Apr 9 03:36:06 2019 Done.
Running the examples in 'seqGetData()':
# of selected samples: 5
# of selected variants: 10
Running the examples in 'seqGetFilter()':
# of selected samples: 5
# of selected variants: 10
Running the examples in 'seqMerge()':
Tue Apr 9 03:36:06 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x269 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: 31977a337486b43ef6f23727c03b93f1]
position [md5: da44a52891c27fdc773a5b99f8c02cf9]
chromosome [md5: b85b07da5fc3648b14c558491bcd05be]
allele [md5: cd5d2fa95a245204b6566b8ec0a8a33a]
genotype [md5: 412d90215ad9bd1c480ce7d58f884844]
phase [md5: 32f9b472c93c5421f2e327b8a2a048ae]
annotation/id [md5: 1365ee5e73e9030aebbee40c7f6bb25b]
annotation/qual [md5: 75d9516e34424c3ba8992777b7daea77]
annotation/filter [md5: faa4243cabb7df18c7e1d768687999de]
annotation/info/AA [md5: a5c30c16b0004b0987c892f4cedfd310]
annotation/info/AC [md5: f1502cc22c0190b135f50c4f149b4e01]
annotation/info/AN [md5: c21269493661db41bb776f4fdacfe74f]
annotation/info/DP [md5: 901bdf13cdb66e0d54005c6e2e1a5b5f]
annotation/info/HM2 [md5: 2fdd6210a1f891a10555ad1d9046d0a2]
annotation/info/HM3 [md5: 86d7e6f95e621ecaa6bbda882cb565e0]
annotation/info/OR [md5: 63361d188cefd769be41d5883d3b814b]
annotation/info/GP [md5: 92a9ae87dfc97e62a19c92f181e9d31f]
annotation/info/BN [md5: 2767eb7baa2d136a1c5987503bb23ee3]
annotation/format/DP [md5: f8694c788d23bbf67cb25ca9b2930709]
Done.
Tue Apr 9 03:36:06 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp1.gds' (46.5K)
# of fragments: 157
save to 'tmp1.gds.tmp'
rename 'tmp1.gds.tmp' (45.5K, reduced: 1.0K)
# of fragments: 69
Tue Apr 9 03:36:06 2019
Tue Apr 9 03:36:06 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: 702b2d499921b2746c717e94c10b850e]
position [md5: 338b3ef9c6450ead1c4eb1d5544aca4a]
chromosome [md5: a4d7b4e4cb2c1f8210a2c71dbab83bb5]
allele [md5: af20c8bbec9c885eb2ec0ac7200bc0fe]
genotype [md5: bb82d3855a2334cf988bce5c6ba94762]
phase [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
annotation/id [md5: a21f24833e38262da8b7d957dd64785a]
annotation/qual [md5: 512c62a8e514115686234183d90daa00]
annotation/filter [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
annotation/info/AA [md5: fe904ec6b205bf8a7884f57507eea0d6]
annotation/info/AC [md5: a651cc76f494587611a9c0e0d46d7839]
annotation/info/AN [md5: 526332c5f7156495d16763e3ae5f1609]
annotation/info/DP [md5: 8c3b67b68611ac59dd89a719e4fc515a]
annotation/info/HM2 [md5: 227879b1605bf8aef6b7d50b80127a3e]
annotation/info/HM3 [md5: 497750adc263e37255ff533a56c7a7b5]
annotation/info/OR [md5: f08c7fb2e2b68d0be4536db007f3488e]
annotation/info/GP [md5: 5ae337da74c76dce7ee5cd06c22c89ff]
annotation/info/BN [md5: 9244facc8572ffd3afbfed7db94c9412]
annotation/format/DP [md5: 49fc303177a01aa04578f0c0bb45ff94]
Done.
Tue Apr 9 03:36:06 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp2.gds' (46.3K)
# of fragments: 157
save to 'tmp2.gds.tmp'
rename 'tmp2.gds.tmp' (45.2K, reduced: 1.0K)
# of fragments: 69
Tue Apr 9 03:36:06 2019
Tue Apr 9 03:36:06 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x269 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: 79a9e2f03ab2a7992e93875c4cbf102d]
position [md5: 0774b9eeec510b900096be5d427cb3ba]
chromosome [md5: 14fc6ae2c5a3415c76c898555dcb5a16]
allele [md5: 084f88745d3947ed533e40271e1ea0d8]
genotype [md5: d414371adf89b3f6df652c23ae4e8ad3]
phase [md5: 32f9b472c93c5421f2e327b8a2a048ae]
annotation/id [md5: e3dbfc9e19459fd1eaf1f937b618a75b]
annotation/qual [md5: 75d9516e34424c3ba8992777b7daea77]
annotation/filter [md5: faa4243cabb7df18c7e1d768687999de]
annotation/info/AA [md5: 247fc1c43d33e10e2314255ca8683d69]
annotation/info/AC [md5: 1ccad5fd3121aaba325fbf501cc887ad]
annotation/info/AN [md5: da9c38467822d68e654fecb3bf9f3498]
annotation/info/DP [md5: 88b66f79339f655db1bb5699aaa670b2]
annotation/info/HM2 [md5: 691d8e114b6e4a3922c686e83f0871fa]
annotation/info/HM3 [md5: 33bb00f6c0fd2f9429825fc35329f076]
annotation/info/OR [md5: 3f5a355124218a349a40c13845212e02]
annotation/info/GP [md5: f165316874ce73a46652b5eb7de29d86]
annotation/info/BN [md5: 0234c15cbc2849ab0bf61cb55fa874c5]
annotation/format/DP [md5: 5ee17f959e045d7d71eb241e51c69c6f]
Done.
Tue Apr 9 03:36:06 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp3.gds' (46.6K)
# of fragments: 157
save to 'tmp3.gds.tmp'
rename 'tmp3.gds.tmp' (45.5K, reduced: 1.0K)
# of fragments: 69
Tue Apr 9 03:36:06 2019
Tue Apr 9 03:36:06 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: 596deceba4d6785759026d710ebbd6a5]
position [md5: 56e4e9c99e7a25933ea668686f3c81f1]
chromosome [md5: 0b766775d21b6b368c399aa2363946c5]
allele [md5: e8dc9d008e28d70c9014929bec8a72b8]
genotype [md5: 6f5d76b39c423e14bbce491ea5a5942b]
phase [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
annotation/id [md5: b666b21b581036b7f45f2753d389058b]
annotation/qual [md5: 512c62a8e514115686234183d90daa00]
annotation/filter [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
annotation/info/AA [md5: 136d498f7dc4879feeb9a03a3cf328fb]
annotation/info/AC [md5: 54348b0efa93fd1f7eb9d7b2767aa761]
annotation/info/AN [md5: bdbca84358d9cf22f172fb8e1a691531]
annotation/info/DP [md5: 7da7dae10b066a3b8e7bb7d6b070a2e8]
annotation/info/HM2 [md5: 4db37a5a26c42890df37b183db37eac7]
annotation/info/HM3 [md5: 3acca3d02fc51ef797290eb4857d35dd]
annotation/info/OR [md5: ea4ef9649f92c784e68a18294a4320be]
annotation/info/GP [md5: 2c66df855998e4c0715f2543a9b60672]
annotation/info/BN [md5: 463eb1f0a504213b9b86b3001315276b]
annotation/format/DP [md5: 34ac9d047be4554124d58b90d8e6abce]
Done.
Tue Apr 9 03:36:07 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp4.gds' (46.3K)
# of fragments: 157
save to 'tmp4.gds.tmp'
rename 'tmp4.gds.tmp' (45.3K, reduced: 1.0K)
# of fragments: 69
Tue Apr 9 03:36:07 2019
Tue Apr 9 03:36:07 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp5.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: bd7a9ec44d55514be411d70be3bc90b6]
position [md5: 787e53edad459d397d89f6572140398c]
chromosome [md5: 15b81663ef97a0890c343b8593ece496]
allele [md5: fc7e212f40d47b068f5a79f4624a094e]
genotype [md5: 3d8d5a11811c6b9259f1a51982bf5966]
phase [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
annotation/id [md5: c9473ed3210534e6b2e098cbf7c8ec34]
annotation/qual [md5: 512c62a8e514115686234183d90daa00]
annotation/filter [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
annotation/info/AA [md5: 77d5bcba4cb9ddc850ed1c13a01b17e7]
annotation/info/AC [md5: 19da63c0f0346353823ceb623b51fe9f]
annotation/info/AN [md5: 58a283bc70b7686719d659802434a4a3]
annotation/info/DP [md5: 438abf141332861815e877f5e4459bed]
annotation/info/HM2 [md5: 725882b2b1b79c80db0ef0f9757c5b9e]
annotation/info/HM3 [md5: 61e24df355c65a28074a344a874b7752]
annotation/info/OR [md5: b2bd6e5fda0e9a34705366f32b2cb6e4]
annotation/info/GP [md5: 47bd1383bc6a8e0591b7083cf4414494]
annotation/info/BN [md5: 4025eb570a89b5d0b7ccc571a94a0d40]
annotation/format/DP [md5: 5d164565b2a5cee1a3be107de4da8876]
Done.
Tue Apr 9 03:36:07 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp5.gds' (44.3K)
# of fragments: 157
save to 'tmp5.gds.tmp'
rename 'tmp5.gds.tmp' (43.3K, reduced: 1.0K)
# of fragments: 69
Tue Apr 9 03:36:07 2019
Tue Apr 9 03:36:07 2019
Preparing merging 5 GDS files:
opening 'tmp1.gds'
opening 'tmp2.gds'
opening 'tmp3.gds'
opening 'tmp4.gds'
opening 'tmp5.gds'
230,237 bytes in total
90 samples in total (90 samples in common)
[1 ] tmp1.gds (269 variants)
[2 ] tmp2.gds (270 variants)
[3 ] tmp3.gds (269 variants)
[4 ] tmp4.gds (270 variants)
[5 ] tmp5.gds (270 variants)
1,348 variants in total, 0 variant in common
Output:
/home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Variables:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype, phase [1,2,3,4,5]
[md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
[md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info (AA,AC,AN,DP,HM2,HM3,OR,GP,BN)
AA [md5: 6df3bcf4c07db5b94be51d1842154038]
AC [md5: 32e0060f853f014a2f0500092eb41a93]
AN [md5: 520c98d2b93738bf522425c1bab724d4]
DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
HM2 [md5: 38b58906766fb24600273356a0db9c50]
HM3 [md5: 2125043130d80f3773acf690705b85e2]
OR [md5: e1829aa0fc0a84250f873500c0174857]
GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format (DP)
DP [1,2,3,4,5] [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
sample.annotation ()
Done.
Tue Apr 9 03:36:07 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.4K)
# of fragments: 153
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.5K, reduced: 996B)
# of fragments: 70
Tue Apr 9 03:36:07 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99
Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62
Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54
Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
<None>
Tue Apr 9 03:36:07 2019
Preparing merging 2 GDS files:
opening '/home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds'
opening 'test.gds'
612,969 bytes in total
180 samples in total (0 sample in common)
[1 ] CEU_Exon.gds (1,348 variants)
[2 ] test.gds (1,348 variants)
1,348 variants in total, 1,348 variants in common
Output:
/home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/output.gds
Variables:
sample.id [md5: 43f95e0eb5cfeff96c9872fd6ab895e4]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [<<<<<<<<<<<<<<<<<<<<<<<<<] [md5: 38110ba7c478e8e77a63637a77388330]
phase [<<<<<<<<<<<<<<<<<<<<<<<<<] [md5: 0eacab6c079033d11dcd127d9139de73]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info (AA,AC,AN,DP,HM2,HM3,OR,GP,BN)
AA [md5: 6df3bcf4c07db5b94be51d1842154038]
AC [md5: 32e0060f853f014a2f0500092eb41a93]
AN [md5: 520c98d2b93738bf522425c1bab724d4]
DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
HM2 [md5: 38b58906766fb24600273356a0db9c50]
HM3 [md5: 2125043130d80f3773acf690705b85e2]
OR [md5: e1829aa0fc0a84250f873500c0174857]
GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format (DP)
DP [<<<<<<<<<<<<<<<<<<<<<<<<<] [md5: 2d4b87bb2cfabb8bb1c1cd633e25cd5c]
sample.annotation (family)
family [md5: 18a957ad99f19f3bedab5893bfc237bf]
Done.
Tue Apr 9 03:36:07 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'output.gds' (244.4K)
# of fragments: 157
save to 'output.gds.tmp'
rename 'output.gds.tmp' (243.4K, reduced: 1.0K)
# of fragments: 71
Tue Apr 9 03:36:07 2019
Running the examples in 'seqMissing()':
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Running the examples in 'seqNumAllele()':
Running the examples in 'seqOpen()':
Running the examples in 'seqOptimize()':
Tue Apr 9 03:36:07 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:07 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.5K)
# of fragments: 159
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:07 2019
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/DP' ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (333.3K)
# of fragments: 86
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (333.2K, reduced: 108B)
# of fragments: 77
Running the examples in 'seqParallel()':
Enable the computing cluster with 2 forked R processes.
Stop the computing cluster.
Running the examples in 'seqParallelSetup()':
Enable the computing cluster with 2 forked R processes.
Stop the computing cluster.
Running the examples in 'seqRecompress()':
Open 'tmp.gds' ...
sample.id (deflated 0.4%) ac460b05cf0de81d3a307259fb908238
variant.id (deflated 0.1%) c9602a5420b6a5a148f5a0120a8750e1
position (deflated 0.0%) a23801beb47fb2d7ca26b65d2b71e622
chromosome (deflated 0.6%) a46ad5529a68298eb581c7c66b31b99b
allele (deflated 0.1%) e65988a36b2675d1e4f6a9ad9d2774a9
genotype/data (deflated 0.0%) 318c71bd2c1878e7d05c6e4b8b3067ef
genotype/˜data (deflated 0.0%)
genotype/@data (deflated 1.0%) e4bff5c57a2a343d93a9a1462b13bc8f
phase/data (deflated 0.7%) 4873107397a2eec80cca77d8fa09592b
phase/˜data (deflated 0.7%)
annotation/id (deflated 0.0%) 164df6a971c24c99ad386bbaf8759cb2
annotation/qual (deflated 0.8%) ff3b3c516fe7081c406d4c26782b44e4
annotation/filter (deflated 0.8%) 5b09a6e58b307857c38e3d82284dfff0
annotation/info/AA (deflated 0.1%) 7bba129ada9e50a98db7451044abdde9
annotation/info/@AA (deflated 0.8%) 5b09a6e58b307857c38e3d82284dfff0
annotation/info/AC (deflated 0.1%) 79076139f25b3f78164182af5d86c680
annotation/info/AN (deflated 0.1%) b4c305461e62a78dc439f7a1df50e5fc
annotation/info/DP (deflated 0.0%) 9f358649989b5fd48fba25b6b50af02f
annotation/info/HM2 (deflated 0.4%) 9b792cdd10840bdda63d77a1ce065588
annotation/info/HM3 (deflated 0.4%) b936dc73a3ffa1241305dfdcc14d71e1
annotation/info/OR (deflated 0.3%) 6f6f800d686268b592ac50f10c5851b9
annotation/info/GP (deflated 0.0%) a1ccfb37b78edd2bb1204c8b9c901b0a
annotation/info/BN (deflated 0.1%) 0ac62828c0c8d3d27cbd15aa975532fd
annotation/format/DP/data (deflated 0.0%) 1f03a59e8b55049b80f6ae42da163783
annotation/format/DP/˜data (deflated 0.0%)
annotation/format/DP/@data (deflated 0.8%) 5b09a6e58b307857c38e3d82284dfff0
sample.annotation/family (deflated 0.5%)
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (299.1K)
# of fragments: 77
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (299.0K, reduced: 27B)
# of fragments: 77
Running the examples in 'seqResetVariantID()':
[ 1] tmp1.gds ... [md5: c9602a5420b6a5a148f5a0120a8750e1]
set new variant id: 1 ... 1348 [1348]
[ 2] tmp2.gds ... [md5: 451be93e6c11061778420ac2850636f1]
set new variant id: 1349 ... 2696 [1348]
Running the examples in 'seqSNP2GDS()':
Tue Apr 9 03:36:09 2019
SNP GDS to SeqArray GDS Format:
sample.id [md5: 8c16d801816b5acb9884930d1a61d479]
variant.id [md5: f82f4a0ec8ea0bef03f2fee13f7bdca5]
position [md5: 52c1144a14a83c5baa5c046dd637b7ca]
chromosome [md5: 95eec41652f7b63bc66f113836a28607]
genotype [md5: 9848dc57cdeff87e29d09b8341c41651]
allele [md5: ac3d0e4abdc8ac4bf6db6832fa3cc79a]
phase [md5: a759f1581057a88d45a9c4194b0b43a3]
annotation/id [md5: 244319c29efb59f5b7a09584a2bbf9bd]
sample.annotation
sample.annotation/family.id [md5: dd38a34e070d5d4ca3c8322c2cfc41d7]
sample.annotation/father.id [md5: 99d5f5add61e93d35fe7f928a524a53b]
sample.annotation/mother.id [md5: 75bf5e4263df975637ddd055360ba593]
sample.annotation/sex [md5: a3615c4ac39a9f121c5eb897dc608495]
sample.annotation/pop.group [md5: 99a5577d77e6a3dbd9d3e1993a380b52]
Done.
Tue Apr 9 03:36:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (464.5K)
# of fragments: 95
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (464.0K, reduced: 564B)
# of fragments: 48
Tue Apr 9 03:36:11 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: unknown
Ploidy: 2
Number of samples: 279
Number of variants: 9,088
Chromosomes:
Chr1 : 716, Chr2 : 742, Chr3 : 609, Chr4 : 562, Chr5 : 566, Chr6 : 565
Chr7 : 472, Chr8 : 488, Chr9 : 416, Chr10: 483, Chr11: 447, Chr12: 427
Chr13: 344, Chr14: 282, Chr15: 262, Chr16: 278, Chr17: 207, Chr18: 266
Chr19: 120, Chr20: 229, Chr21: 126, Chr22: 116, Chr23: 365
Alleles:
ALT: <None>
tabulation: 2, 9088(100.0%)
Annotation, Quality:
Min: 100, 1st Qu: 100, Median: 100, Mean: 100, 3rd Qu: 100, Max: 100
Annotation, FILTER:
PASS, All filters passed, 9088(100.0%)
Annotation, INFO variable(s):
<None>
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
Annotation, sample variable(s):
family.id, String, <NA>
father.id, String, <NA>
mother.id, String, <NA>
sex, String, <NA>
pop.group, String, <NA>
Running the examples in 'seqSetFilter-methods()':
Running the examples in 'seqSetFilterCond()':
# of selected variants: 241
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
# of selected variants: 98
# of selected variants: 241
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
# of selected variants: 72
Running the examples in 'seqStorageOption()':
Tue Apr 9 03:36:11 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
# of samples: 90
Output:
tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp1.gds' (185.5K)
# of fragments: 159
save to 'tmp1.gds.tmp'
rename 'tmp1.gds.tmp' (184.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:11 2019
Tue Apr 9 03:36:11 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
# of samples: 90
Output:
tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: 01bb26dcaafd0df48a31602185b65c92]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: f63a4d4efe99e6acab979b74d35136cb]
genotype [md5: 61b541faecd37d86a354a0020b754ce1]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: 91c1d0a0ac5571c0226fbd8727b114f1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: bc40b5045fcd40de3b0be5e513e5e836]
annotation/info/AC [md5: d428a081a2f32ecc51bf01762743e217]
annotation/info/AN [md5: 758c32f9b396ff0d4697a362ff2d6dea]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: 7b7f8128d98d09f9183737df1d1a6a0a]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: be4b0b7b40783bb7933c366bc39f218a]
annotation/format/DP [md5: ad5f45b991605297330efdb18bc6a268]
Done.
Tue Apr 9 03:36:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp2.gds' (184.6K)
# of fragments: 159
save to 'tmp2.gds.tmp'
rename 'tmp2.gds.tmp' (183.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:11 2019
Tue Apr 9 03:36:11 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
# of samples: 90
Output:
tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348, 59.2K }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 8070a7f5f2e17ee4435fbb45466e8213]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp3.gds' (228.1K)
# of fragments: 151
save to 'tmp3.gds.tmp'
rename 'tmp3.gds.tmp' (227.2K, reduced: 996B)
# of fragments: 68
Tue Apr 9 03:36:11 2019
Tue Apr 9 03:36:11 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
# of samples: 90
Output:
tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 LZ4_ra, 20B }
Digests:
sample.id [md5: a7b2eb225e6552690973f2f1b79dc73e]
variant.id [md5: 9f99987c0bc8217713b4a8a55a153626]
position [md5: 2499d10bd9660eafde7dadcb64988691]
chromosome [md5: 1e20e040c376abdd54f7851023ba4bab]
allele [md5: 072e0e67eb949fcf2eba36e2de04ffed]
genotype [md5: ca8fa50513a5500dfd5f39cf6a1e749b]
phase [md5: 54b8a7f61c639556b75e22340c45e276]
annotation/id [md5: 7ff9f8150de634e5a98b7b975268c968]
annotation/qual [md5: 2d95cddb8b3f3555f0d5db4d7140979c]
annotation/filter [md5: f9941c922320aca8ff482466453cfc9a]
annotation/info/AA [md5: b493afbacec86f22050ae823486328cc]
annotation/info/AC [md5: d318f101c7e5f9b1915566e07d9d18e9]
annotation/info/AN [md5: e503620a86e357b5f557a270b9d86f29]
annotation/info/DP [md5: 7f0b1f9249325d70688cd329b2c68405]
annotation/info/HM2 [md5: 4423a47770a5636e1f90f02c41adc9cc]
annotation/info/HM3 [md5: 4f1323efa931fa98f38a80a53f4bb1da]
annotation/info/OR [md5: d72964829bbd1d23736c625b279985d0]
annotation/info/GP [md5: 2e0f54a5b11378c554da151824da40ff]
annotation/info/BN [md5: 31d0303d62a38abc7d029484956188cb]
annotation/format/DP [md5: 0520c9ff2cc9ca7f51000500430b75d6]
Done.
Tue Apr 9 03:36:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp4.gds' (234.6K)
# of fragments: 159
save to 'tmp4.gds.tmp'
rename 'tmp4.gds.tmp' (233.6K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:11 2019
Running the examples in 'seqSummary()':
File: /home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99
Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62
Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54
Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
family, String, <NA>
File: /home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Sample ID: no duplicate.
sample.id: 'md5' [OK]
Variant ID: no duplicate.
variant.id: 'md5' [OK]
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Genotypes:
genotype/data: 'md5' [OK]
genotype/˜data: no digest
genotype/@data: 'md5' [OK]
position: 'md5' [OK]
Chromosomes:
Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99
Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62
Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54
Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23
chromosome: 'md5' [OK]
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
chromosome: 'md5' [OK]
Annotation, ID:
annotation/id: 'md5' [OK]
Annotation, Quality:
Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
annotation/qual: 'md5' [OK]
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
family, String, <NA>
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Number of selected samples: 90
Number of selected variants: 1,348
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
family, String, <NA>
Reference: human_b36_both.fasta
Annotation, FILTER:
PASS, All filters passed, 1348(100.0%)
q10, Quality below 10, 0(0.0%)
Alleles:
ALT: <None>
Annotation, INFO variable(s):
AA, ., String, Ancestral Allele
AC, 1, Integer, Total number of alternate alleles in called genotypes
AN, 1, Integer, Total number of alleles in called genotypes
DP, 1, Integer, Total Depth
HM2, 0, Flag, HapMap2 membership
HM3, 0, Flag, HapMap3 membership
OR, 1, String, Previous rs number
GP, 1, String, GRCh37 position(s)
BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
GT, 1, String, Genotype
DP, ., Integer, Read Depth from MOSAIK BAM
# of selected samples: 5
# of selected variants: 10
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Number of selected samples: 5
Number of selected variants: 10
Running the examples in 'seqSystem()':
Running the examples in 'seqTranspose()':
Tue Apr 9 03:36:11 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.5K)
# of fragments: 159
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:12 2019
Running the examples in 'seqVCF2GDS()':
Tue Apr 9 03:36:12 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.5K)
# of fragments: 159
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
# of fragments: 70
Tue Apr 9 03:36:12 2019
Tue Apr 9 03:36:12 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
calculating the total number of variants ...
the total number of variants for import: 1,348
Writing to 2 files:
tmp_p2_tmp01_14ce507a1175 [1..674]
tmp_p2_tmp02_14ced5443fe [675..1,348]
Done (Tue Apr 9 03:36:12 2019).
Output:
tmp_p2.gds
Merging:
opening 'tmp_p2_tmp01_14ce507a1175' ... [done]
opening 'tmp_p2_tmp02_14ced5443fe' ... [done]
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: fe72c1ff1844ce8eb7db6b1392f59dfa]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/info/AA [md5: 6df3bcf4c07db5b94be51d1842154038]
annotation/info/AC [md5: 32e0060f853f014a2f0500092eb41a93]
annotation/info/AN [md5: 520c98d2b93738bf522425c1bab724d4]
annotation/info/DP [md5: a304721e223a79637ccedb5b5a6f2f8f]
annotation/info/HM2 [md5: 38b58906766fb24600273356a0db9c50]
annotation/info/HM3 [md5: 2125043130d80f3773acf690705b85e2]
annotation/info/OR [md5: e1829aa0fc0a84250f873500c0174857]
annotation/info/GP [md5: 7b29009823b6f3d1beb4afac91ce11a5]
annotation/info/BN [md5: 05f5e42981b9671fa0f931cd19d61339]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp_p2.gds' (185.6K)
# of fragments: 160
save to 'tmp_p2.gds.tmp'
rename 'tmp_p2.gds.tmp' (184.6K, reduced: 1.1K)
# of fragments: 70
Tue Apr 9 03:36:12 2019
Tue Apr 9 03:36:12 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
annotation/format/DP [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Tue Apr 9 03:36:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (168.4K)
# of fragments: 100
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (167.8K, reduced: 600B)
# of fragments: 50
Tue Apr 9 03:36:12 2019
Tue Apr 9 03:36:12 2019
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (243.4K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
# of samples: 90
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
sample.id [md5: d4d5be5fd4dc15775186933a968eeb86]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: f3c7091eb406b90b71be6234c1b996f2]
chromosome [md5: b65ee00d30fd4019558a228e14144303]
allele [md5: 9217bde736ad7a49d70b5788074a2f33]
genotype [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
phase [md5: f272efd2132d769ded473e188c68a710]
annotation/id [md5: ad224facbbf907a362af31fa4d9f8cf1]
annotation/qual [md5: 61fe29d41ab53d2a877966fca27ae725]
annotation/filter [md5: 87214e07213369b019511967d315e61b]
Done.
Tue Apr 9 03:36:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (37.3K)
# of fragments: 87
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (36.8K, reduced: 516B)
# of fragments: 44
Tue Apr 9 03:36:12 2019
Running the examples in 'seqVCF_Header()':
Running the examples in 'seqVCF_SampID()':
# of selected variants: 898
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
RUNIT TEST PROTOCOL -- Tue Apr 9 03:37:06 2019
***********************************************
Number of test functions: 27
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures
Number of test functions: 27
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
82.756 3.629 86.118
