Issue when running on WGS vcf file

[anh151]

• Do you want to request a feature or report a bug? Report a bug maybe

• What is the current behavior? I am able to get pharmcat to execute properly with an array vcf file, but I can't replicate the same behavior for a WGS vcf file using the exact same command. I tried to follow the traceback but was unsuccessful.

• If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar.

  output_vcf = f"{bucket}/hail/1111111_wgs.vcf.gz"
  vcf_file_compressed = "1111111_wgs.vcf.gz"
  vcf_file = "111111_wgs.vcf"
  !gsutil cp {output_vcf} ./
  !gunzip {vcf_file_compressed}
  output_file = output + "1111111_wgs.json"
  !java -cp {pharmcat} org.pharmgkb.pharmcat.phenotype.Phenotyper -vcf {vcf_file} -f {output_file}

  Exception in thread "main" java.lang.IllegalArgumentException: Number of keys does not match number of values
  at com.google.common.base.Preconditions.checkArgument(Preconditions.java:142)
  at org.pharmgkb.parser.vcf.model.VcfSample.<init>(VcfSample.java:28)
  at org.pharmgkb.parser.vcf.VcfParser.parseNextLine(VcfParser.java:239)
  at org.pharmgkb.parser.vcf.VcfParser.parse(VcfParser.java:127)
  at org.pharmgkb.pharmcat.haplotype.VcfReader.read(VcfReader.java:117)
  at org.pharmgkb.pharmcat.haplotype.VcfReader.<init>(VcfReader.java:59)
  at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.buildVcfReader(NamedAlleleMatcher.java:121)
  at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.call(NamedAlleleMatcher.java:162)
  at org.pharmgkb.pharmcat.phenotype.Phenotyper.main(Phenotyper.java:72)
  Total elapsed time in seconds: 1.8486080169677734

• Please tell us about your environment:

  • PharmCAT Version: 0.8
  • JDK Version: openjdk version "11.0.12" 2021-07-20 OpenJDK Runtime Environment Temurin-11.0.12+7 (build 11.0.12+7) OpenJDK 64-Bit Server VM Temurin-11.0.12+7 (build 11.0.12+7, mixed mode)
  • Environment: linux

[markwoon]

This error happens when the FORMAT column and the sample column in the VCF do not have the same number of elements.

For example:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample
chr1    97078987    rs114096998 G   T   .   PASS    .   GT  0/0
chr1    97078987    rs114096998 G   T   .   FAIL    .   GT:GQ   0/0
chr1    97078987    rs114096998 G   T   .   FAIL    .   .   0/0

The first line is correct (1 entry in format, 1 entry in sample). The second line fails because there are 2 entries in format, 1 entry in sample. The third line fails because there are 0 entries in format, 1 entry in sample.

I'm closing this issue for now. If this is not the case, please reopen with a sample of the VCF data containing the problem. Please make sure the VCF data is anonymized.

FYI, we just released 1.0 and encourage you to update to the latest version.