[Bioc-devel] VariantAnnotation: verbose output of readVcf
Julian Gehring
julian.gehring at embl.de
Thu Jul 16 11:35:19 CEST 2015
Hi,
In recent versions of 'VariantAnnotation', the 'readVcf' function prints
information about the header lines:
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
shows
found header lines for 3 ‘fixed’ fields: ALT, QUAL, FILTER
found header lines for 6 ‘info’ fields: NS, DP, AF, AA, DB, H2
found header lines for 4 ‘geno’ fields: GT, GQ, DP, HQ
When one reads a VCF in chunks, this gets displayed once per chunk:
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="ALT", geno=c("GT", "GL"), info=c("LDAF"))
tab <- TabixFile(fl, yieldSize=4000)
open(tab)
while (nrow(vcf_yield <- readVcf(tab, "hg19", param=param)))
cat("vcf dim:", dim(vcf), "\n")
found header lines for 1 ‘fixed’ fields: ALT
found header lines for 1 ‘info’ fields: LDAF
found header lines for 2 ‘geno’ fields: GT, GL
vcf dim: 5 3
found header lines for 1 ‘fixed’ fields: ALT
found header lines for 1 ‘info’ fields: LDAF
found header lines for 2 ‘geno’ fields: GT, GL
vcf dim: 5 3
found header lines for 1 ‘fixed’ fields: ALT
found header lines for 1 ‘info’ fields: LDAF
found header lines for 2 ‘geno’ fields: GT, GL
vcf dim: 5 3
found header lines for 1 ‘fixed’ fields: ALT
found header lines for 1 ‘info’ fields: LDAF
found header lines for 2 ‘geno’ fields: GT, GL
For larger files, this get a bit cumbersome. It looks to me like debug
information. Is this behavior intentional?
Best wishes
Julian
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