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  1. Barna Package
  2. BARNA-389

astalavista scorer requires chromosome names to start with "chr"

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    Details

    • Type: Story
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: AStalavista 3.2 (API 1.22)
    • Fix Version/s: None
    • Component/s: Astalavista
    • Labels:
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      Description

      AStalavista Scorer assumes chromosome names always start with "chr". This is a problem when using reference genomes that use only the chromosome number, like the 1000 genomes project does.

      When using GTF, VCF & reference sequence FASTA files that use chromosome numbers without the "chr" prefix, this Java exception occurs:

      [ERROR] String index out of range: -2
      java.lang.StringIndexOutOfBoundsException: String index out of range: -2
      at java.lang.String.substring(String.java:1931)
      at barna.astalavista.Scorer.getVariants(Scorer.java:435)
      at barna.astalavista.Scorer.scoreSites(Scorer.java:1012)
      at barna.astalavista.Scorer.callLoop(Scorer.java:145)
      at barna.astalavista.AStalavista.call(AStalavista.java:131)
      at barna.astalavista.Scorer.call(Scorer.java:134)
      at barna.astalavista.Scorer.call(Scorer.java:31)
      at barna.commons.launcher.Flux.main(Flux.java:198)

      Note: This "chr" prefix requirement is documented on the scorer confluence wiki:
      http://sammeth.net/confluence/pages/viewpage.action?pageId=5177671
      but can still be considered a bug due to the prevalence of VCF files that do not use this prefix.

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            Assignee:
            micha Micha Sammeth
            Reporter:
            martin Martin Oti
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              Dates

              Created:
              Updated: