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> if (Sys.info()[['sysname']] != "Windows")
+ {
+ # according to the limit of 32-bit 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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, 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
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 object is masked from 'package:base':
apply
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
# of selected samples: 5
# of selected variants: 10
Running the examples in 'KG_P1_SampData()':
Running the examples in 'SeqArray-package()':
Thu Apr 12 02:52:54 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:54 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.1K)
# of fragments: 154
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:52:54 2018
File: /home/biocbuild/bbs-3.6-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,] 0 0 0 0 0
[2,] 0 0 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs114199731"
$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] "rs35583437"
$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] "rs12347"
$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] "rs41269293"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 NA 1 0 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2072183"
$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] "rs4253027"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 1 1 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2490763"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
$phase
[1] 0 0 0 0 0
$qual
[1] "rs11180483"
$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] "rs35349730"
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 0 0 0
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs62078800"
# 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,] 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,] 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,] 1 NA 1 0 1
[2,] 0 NA 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 NA 1 1 1
[2,] 0 NA 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
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 NA 0 0 0
[2,] 0 NA 0 0 0
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,] 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,] 01 ff 01 00 01
[2,] 00 ff 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 ff 01 01 01
[2,] 00 ff 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 01 01 01 00 01
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 ff 00 00 00
[2,] 00 ff 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 1 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 NA 0 NA 0 0 NA
[2,] 0 0 0 0 NA 0 NA 1 0 NA
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 1 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 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 01 00 01 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 ff 00 ff 00 00 ff
[2,] 00 00 00 00 ff 00 ff 01 00 ff
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 01 00 01 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 01 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 01 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
$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] "rs114199731"
$DP
index
sample [,1]
[1,] 1
[2,] 11
[3,] 52
[4,] 53
[5,] 26
$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] "rs35583437"
$DP
index
sample [,1]
[1,] 7
[2,] 5
[3,] 14
[4,] 24
[5,] 191
$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] "rs12347"
$DP
index
sample [,1]
[1,] 12
[2,] 79
[3,] 31
[4,] 70
[5,] 133
$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] "rs41269293"
$DP
index
sample [,1]
[1,] 18
[2,] 34
[3,] 56
[4,] 29
[5,] 111
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 NA 1 0 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2072183"
$DP
index
sample [,1]
[1,] 15
[2,] 21
[3,] 31
[4,] 68
[5,] 149
$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] "rs4253027"
$DP
index
sample [,1]
[1,] 2
[2,] 59
[3,] 30
[4,] 67
[5,] 37
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 1 1 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2490763"
$DP
index
sample [,1]
[1,] 21
[2,] 68
[3,] 40
[4,] 43
[5,] 64
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
$phase
[1] 0 0 0 0 0
$qual
[1] "rs11180483"
$DP
index
sample [,1]
[1,] 20
[2,] 55
[3,] 17
[4,] 42
[5,] 189
$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] "rs35349730"
$DP
index
sample [,1]
[1,] 9
[2,] 130
[3,] 81
[4,] 44
[5,] 13
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 0 0 0
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs62078800"
$DP
index
sample [,1]
[1,] 3
[2,] 1
[3,] 1
[4,] 27
[5,] 27
0
0
1
0
3
0
3
4
0
0
[1] 1
$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] "rs114199731"
[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
$qual
[1] "rs35583437"
[1] 3
$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] "rs12347"
[1] 4
$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] "rs41269293"
[1] 5
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 1 NA 1 0 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2072183"
[1] 6
$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] "rs4253027"
[1] 7
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 1 1 1
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs2490763"
[1] 8
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
$phase
[1] 0 0 0 0 0
$qual
[1] "rs11180483"
[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
$qual
[1] "rs35349730"
[1] 10
$geno
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 NA 0 0 0
[2,] 0 NA 0 0 0
$phase
[1] 0 0 0 0 0
$qual
[1] "rs62078800"
# 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,] 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,] 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,] 1 NA 1 0 1
[2,] 0 NA 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 NA 1 1 1
[2,] 0 NA 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
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 NA 0 0 0
[2,] 0 NA 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 1 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 NA 0 NA 0 0 NA
[2,] 0 0 0 0 NA 0 NA 1 0 NA
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 1 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 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
$sample.id
[1] "NA06985"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 1 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
$sample.id
[1] "NA06989"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 NA 0 NA 0 0 NA
[2,] 0 0 0 0 NA 0 NA 1 0 NA
$sample.id
[1] "NA07000"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
$sample.id
[1] "NA07048"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
$sample.id
[1] "NA07346"
$genotype
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
Running the examples in 'seqAsVCF()':
Running the examples in 'seqBED2GDS()':
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Thu Apr 12 02:52:54 2018
PLINK BED to SeqArray GDS Format:
BED file: "/home/biocbuild/bbs-3.6-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
FAM file: '/home/biocbuild/bbs-3.6-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz' (60 samples)
BIM file: '/home/biocbuild/bbs-3.6-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.
Thu Apr 12 02:52:55 2018
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
Thu Apr 12 02:52:55 2018
File: /home/biocbuild/bbs-3.6-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,] 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,] 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,] 1 NA 1 0 1
[2,] 0 NA 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 NA 1 1 1
[2,] 0 NA 0 0 0
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 1 1 1 0 1
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 NA 0 0 0
[2,] 0 NA 0 0 0
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,] 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,] 01 ff 01 00 01
[2,] 00 ff 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 ff 01 01 01
[2,] 00 ff 00 00 00
sample
allele [,1] [,2] [,3] [,4] [,5]
[1,] 00 00 00 00 00
[2,] 01 01 01 00 01
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 ff 00 00 00
[2,] 00 ff 00 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 1 0 1 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 NA 0 NA 0 0 NA
[2,] 0 0 0 0 NA 0 NA 1 0 NA
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 1 0 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 0 0 0 0 0 1 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 1 0 0 0
[2,] 0 0 0 0 0 0 0 1 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 01 00 01 00 00 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 ff 00 ff 00 00 ff
[2,] 00 00 00 00 ff 00 ff 01 00 ff
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 01 00 01 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 00 00 00 00 00 00 01 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 01 00 00 00
[2,] 00 00 00 00 00 00 00 01 00 00
variant
sample [,1] [,2] [,3]
[1,] 2 2 1
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
variant
sample [,1] [,2] [,3]
[1,] 2 1 2
[2,] 2 NA 2
[3,] 2 1 2
[4,] 2 2 2
[5,] 2 1 2
variant
sample [,1] [,2] [,3]
[1,] 2 1 2
[2,] NA 1 2
[3,] 1 1 2
[4,] 1 2 2
[5,] 1 1 2
variant
sample [,1]
[1,] 2
[2,] NA
[3,] 2
[4,] 2
[5,] 2
$dos
variant
sample [,1] [,2] [,3]
[1,] 2 2 1
[2,] 2 2 2
[3,] 2 2 2
[4,] 2 2 2
[5,] 2 2 2
$pos
[1] 112960987 48692052 7950283
$dos
variant
sample [,1] [,2] [,3]
[1,] 2 1 2
[2,] 2 NA 2
[3,] 2 1 2
[4,] 2 2 2
[5,] 2 1 2
$pos
[1] 28362841 44545705 50408787
$dos
variant
sample [,1] [,2] [,3]
[1,] 2 1 2
[2,] NA 1 2
[3,] 1 1 2
[4,] 1 2 2
[5,] 1 1 2
$pos
[1] 101635488 74071367 88522150
$dos
variant
sample [,1]
[1,] 2
[2,] NA
[3,] 2
[4,] 2
[5,] 2
$pos
[1] 9877205
Running the examples in 'seqClose-methods()':
Running the examples in 'seqDelete()':
Thu Apr 12 02:52:55 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:55 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.1K)
# of fragments: 154
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:52:55 2018
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' (184.0K)
# of fragments: 66
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (51.4K, reduced: 132.6K)
# of fragments: 54
Running the examples in 'seqDigest()':
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
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: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
position [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
chromosome [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
allele [md5: f770ac938a0865d071f30da0b0fd661d]
genotype [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
[md5: f2b08fa659c10fc5a5582c65f52aa854]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: d3ffc05abf9d714539b72faa0bc8bb21]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
annotation/info/AC [md5: 4659fcd926477e4657010f159031f7f0]
annotation/info/AN [md5: 7612db10f5f04927a15c87c872beaa76]
annotation/info/DP [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
annotation/info/HM2 [md5: e5d63d253a319ea5e1ed341108d45d8b]
annotation/info/HM3 [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
annotation/info/OR [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
annotation/info/GP [md5: 46673c5ba130c5ed45fcf4772eea05f5]
annotation/info/BN [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
annotation/format/DP [md5: a6f12cf35ac873fcc0faf84474689367]
[md5: fd3692517995bcaa0b04ac21bb10e314]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (17.4K)
# of fragments: 145
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (16.6K, reduced: 864B)
# of fragments: 73
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
position [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
chromosome [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
allele [md5: f770ac938a0865d071f30da0b0fd661d]
genotype [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
[md5: f2b08fa659c10fc5a5582c65f52aa854]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: d3ffc05abf9d714539b72faa0bc8bb21]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/format/DP [md5: a6f12cf35ac873fcc0faf84474689367]
[md5: fd3692517995bcaa0b04ac21bb10e314]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (12.1K)
# of fragments: 103
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (11.5K, reduced: 600B)
# of fragments: 53
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
position [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
chromosome [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
allele [md5: f770ac938a0865d071f30da0b0fd661d]
genotype [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
[md5: f2b08fa659c10fc5a5582c65f52aa854]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: d3ffc05abf9d714539b72faa0bc8bb21]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
annotation/info/AC [md5: 4659fcd926477e4657010f159031f7f0]
annotation/info/AN [md5: 7612db10f5f04927a15c87c872beaa76]
annotation/info/DP [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
annotation/info/HM2 [md5: e5d63d253a319ea5e1ed341108d45d8b]
annotation/info/HM3 [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
annotation/info/OR [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
annotation/info/GP [md5: 46673c5ba130c5ed45fcf4772eea05f5]
annotation/info/BN [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
sample.annotation/family [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (14.3K)
# of fragments: 129
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (13.6K, reduced: 756B)
# of fragments: 66
Export to 'tmp.gds'
sample.id (8) [md5: 7269c374a455e3c2d046ce1e3b2854a8]
variant.id (100) [md5: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
position [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
chromosome [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
allele [md5: f770ac938a0865d071f30da0b0fd661d]
genotype [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
[md5: f2b08fa659c10fc5a5582c65f52aa854]
phase [md5: fbfc323ca650cabd3df3affdc857c9da]
[md5: fbfc323ca650cabd3df3affdc857c9da]
annotation/id [md5: d3ffc05abf9d714539b72faa0bc8bb21]
annotation/qual [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
annotation/filter [md5: 155aaa7359e27197a75f997dc645e48d]
annotation/info/AA [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
annotation/info/AC [md5: 4659fcd926477e4657010f159031f7f0]
annotation/info/AN [md5: 7612db10f5f04927a15c87c872beaa76]
annotation/info/DP [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
annotation/info/HM2 [md5: e5d63d253a319ea5e1ed341108d45d8b]
annotation/info/HM3 [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
annotation/info/OR [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
annotation/info/GP [md5: 46673c5ba130c5ed45fcf4772eea05f5]
annotation/info/BN [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
annotation/format/DP [md5: a6f12cf35ac873fcc0faf84474689367]
[md5: fd3692517995bcaa0b04ac21bb10e314]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (17.0K)
# of fragments: 140
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (16.2K, reduced: 828B)
# of fragments: 71
Running the examples in 'seqGDS2SNP()':
Thu Apr 12 02:52:57 2018
SeqArray GDS to SNP GDS Format:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Done.
Thu Apr 12 02:52:57 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (30.3K)
# of fragments: 31
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (30.1K, reduced: 192B)
# of fragments: 15
Thu Apr 12 02:52:57 2018
Running the examples in 'seqGDS2VCF()':
# of selected samples: 5
Thu Apr 12 02:52:57 2018
VCF Export: tmp.vcf.gz
5 samples, 1,348 variants
INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
FORMAT Field: DP
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Thu Apr 12 02:52:57 2018 Done.
Thu Apr 12 02:52:57 2018
VCF Export: tmp1.vcf.gz
5 samples, 1,348 variants
INFO Field: <none>
FORMAT Field: <none>
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Thu Apr 12 02:52:57 2018 Done.
Thu Apr 12 02:52:57 2018
VCF Export: tmp2.vcf.gz
5 samples, 1,348 variants
INFO Field: BN, GP, AA, DP, HM2
FORMAT Field: <none>
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Thu Apr 12 02:52:57 2018 Done.
# of selected samples: 90
# of selected variants: 1,348
Thu Apr 12 02:52:57 2018
VCF Export: tmp.vcf.gz
90 samples, 1,348 variants
INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
FORMAT Field: DP
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed in 0s
Thu Apr 12 02:52:57 2018 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()':
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x269 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp1.gds' (46.2K)
# of fragments: 152
save to 'tmp1.gds.tmp'
rename 'tmp1.gds.tmp' (45.1K, reduced: 1.0K)
# of fragments: 65
Thu Apr 12 02:52:58 2018
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp2.gds' (45.9K)
# of fragments: 152
save to 'tmp2.gds.tmp'
rename 'tmp2.gds.tmp' (44.9K, reduced: 1.0K)
# of fragments: 65
Thu Apr 12 02:52:58 2018
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x269 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp3.gds' (46.2K)
# of fragments: 152
save to 'tmp3.gds.tmp'
rename 'tmp3.gds.tmp' (45.1K, reduced: 1.0K)
# of fragments: 65
Thu Apr 12 02:52:58 2018
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp4.gds' (45.9K)
# of fragments: 152
save to 'tmp4.gds.tmp'
rename 'tmp4.gds.tmp' (44.9K, reduced: 1.0K)
# of fragments: 65
Thu Apr 12 02:52:58 2018
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp5.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x270 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp5.gds' (44.0K)
# of fragments: 152
save to 'tmp5.gds.tmp'
rename 'tmp5.gds.tmp' (42.9K, reduced: 1.0K)
# of fragments: 65
Thu Apr 12 02:52:58 2018
Thu Apr 12 02:52:58 2018
Preparing merging 5 GDS files:
opening 'tmp1.gds' ... [done]
opening 'tmp2.gds' ... [done]
opening 'tmp3.gds' ... [done]
opening 'tmp4.gds' ... [done]
opening 'tmp5.gds' ... [done]
228,388 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-3.6-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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.0K)
# of fragments: 149
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 996B)
# of fragments: 66
Thu Apr 12 02:52:58 2018
File: /home/biocbuild/bbs-3.6-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>
Thu Apr 12 02:52:58 2018
Preparing merging 2 GDS files:
opening '/home/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/SeqArray/extdata/CEU_Exon.gds' ... [done]
opening 'test.gds' ... [done]
612,005 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-3.6-bioc/meat/SeqArray.Rcheck/tests/output.gds
Variables:
sample.id [md5: 43f95e0eb5cfeff96c9872fd6ab895e4]
variant.id [md5: ae004cdebf8eab2e7883a2182caa3967]
position [md5: aab908c919d5d6024d3ba1b7e8951830]
chromosome [md5: 2a27ef622bc33533749d1a2985dc6a4a]
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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'output.gds' (244.7K)
# of fragments: 153
save to 'output.gds.tmp'
rename 'output.gds.tmp' (243.7K, reduced: 1.0K)
# of fragments: 67
Thu Apr 12 02:52:58 2018
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()':
Thu Apr 12 02:52:58 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:52:58 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.1K)
# of fragments: 154
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:52:58 2018
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/DP' ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (332.8K)
# of fragments: 82
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (332.7K, reduced: 108B)
# of fragments: 73
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 'seqSNP2GDS()':
Thu Apr 12 02:52:59 2018
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.
Thu Apr 12 02:53:01 2018
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
Thu Apr 12 02:53:01 2018
File: /home/biocbuild/bbs-3.6-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()':
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
Output:
tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp1.gds' (185.1K)
# of fragments: 154
save to 'tmp1.gds.tmp'
rename 'tmp1.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:01 2018
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
Output:
tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp2.gds' (184.1K)
# of fragments: 154
save to 'tmp2.gds.tmp'
rename 'tmp2.gds.tmp' (183.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:01 2018
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
Output:
tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348, 59.2K }
Hash function 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.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp3.gds' (227.7K)
# of fragments: 146
save to 'tmp3.gds.tmp'
rename 'tmp3.gds.tmp' (226.7K, reduced: 984B)
# of fragments: 64
Thu Apr 12 02:53:01 2018
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: customized
Output:
tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 LZ4_ra, 20B }
Hash function digests:
sample.id [md5: a7b2eb225e6552690973f2f1b79dc73e]
variant.id [md5: 9f99987c0bc8217713b4a8a55a153626]
position [md5: 2499d10bd9660eafde7dadcb64988691]
chromosome [md5: 1e20e040c376abdd54f7851023ba4bab]
allele [md5: 1122d969fd5f1591a58effa1038dda3b]
genotype [md5: 30c2fcc33d9e0a5b42c629bdcc307f5f]
phase [md5: 54b8a7f61c639556b75e22340c45e276]
annotation/id [md5: 945dc5acd51d875f792a8f4e5a846afa]
annotation/qual [md5: 2d95cddb8b3f3555f0d5db4d7140979c]
annotation/filter [md5: f9941c922320aca8ff482466453cfc9a]
annotation/info/AA [md5: b493afbacec86f22050ae823486328cc]
annotation/info/AC [md5: d318f101c7e5f9b1915566e07d9d18e9]
annotation/info/AN [md5: 336c3c85a089ac2dca4d764c2a25aa1f]
annotation/info/DP [md5: 7f0b1f9249325d70688cd329b2c68405]
annotation/info/HM2 [md5: 4423a47770a5636e1f90f02c41adc9cc]
annotation/info/HM3 [md5: 4f1323efa931fa98f38a80a53f4bb1da]
annotation/info/OR [md5: 1079eaa7ad2d24a2c3ba7f7da8b25e11]
annotation/info/GP [md5: 2e0f54a5b11378c554da151824da40ff]
annotation/info/BN [md5: 1c1d591ea2f9e6bd1ae986dd73f4120e]
annotation/format/DP [md5: 0520c9ff2cc9ca7f51000500430b75d6]
Done.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp4.gds' (234.3K)
# of fragments: 154
save to 'tmp4.gds.tmp'
rename 'tmp4.gds.tmp' (233.2K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:01 2018
Running the examples in 'seqSummary()':
File: /home/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/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-3.6-bioc/meat/SeqArray.Rcheck/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Sample ID: no duplicate.
sample.id: 'md5' passes
Variant ID: no duplicate.
variant.id: 'md5' passes
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Genotypes:
genotype/data: 'md5' passes
genotype/˜data: no digest
genotype/@data: 'md5' passes
position: 'md5' passes
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' passes
Alleles:
ALT: <None>
tabulation: 2, 1346(99.9%); 3, 2(0.1%)
chromosome: 'md5' passes
Annotation, ID:
annotation/id: 'md5' passes
Annotation, Quality:
Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
annotation/qual: 'md5' passes
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()':
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.1K)
# of fragments: 154
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:01 2018
Running the examples in 'seqVCF2GDS()':
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (185.1K)
# of fragments: 154
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:01 2018
Thu Apr 12 02:53:01 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
calculating the total number of variants ...
the total number of variants for import: 1,348
Writing to 2 files:
tmp_p2_tmp01_62322614437b [1..674]
tmp_p2_tmp02_62325e7a4696 [675..1,348]
Done (Thu Apr 12 02:53:02 2018).
Output:
tmp_p2.gds
Merging:
opening 'tmp_p2_tmp01_62322614437b' ... [done]
opening 'tmp_p2_tmp02_62325e7a4696' ... [done]
Hash function 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.
Thu Apr 12 02:53:02 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp_p2.gds' (185.2K)
# of fragments: 155
save to 'tmp_p2.gds.tmp'
rename 'tmp_p2.gds.tmp' (184.1K, reduced: 1.0K)
# of fragments: 66
Thu Apr 12 02:53:02 2018
Thu Apr 12 02:53:02 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:02 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (167.9K)
# of fragments: 95
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (167.3K, reduced: 588B)
# of fragments: 46
Thu Apr 12 02:53:02 2018
Thu Apr 12 02:53:02 2018
Variant Call Format (VCF) Import:
file(s):
CEU_Exon.vcf.gz (226.0K)
file format: VCFv4.0
the number of sets of chromosomes (ploidy): 2
the number of samples: 90
genotype storage: bit2
compression method: ZIP_RA
Output:
tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data { Bit2 2x90x1348 ZIP_ra, 16B }
Hash function 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.
Thu Apr 12 02:53:02 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'tmp.gds' (36.8K)
# of fragments: 82
save to 'tmp.gds.tmp'
rename 'tmp.gds.tmp' (36.3K, reduced: 504B)
# of fragments: 40
Thu Apr 12 02:53:02 2018
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 -- Thu Apr 12 02:53:54 2018
***********************************************
Number of test functions: 26
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqArray RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
78.600 4.404 82.745
