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  1. Barna Package
  2. BARNA-378

Scorer extracts wrong genomic sequence

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    Details

    • Type: Bug
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: AStalavista 3.2 (API 1.22)
    • Fix Version/s: None
    • Component/s: Astalavista
    • Labels:
      None

      Description

      Scorer extracts a sequence that does not agree with the reference given in the VCF file. Error is:

      [ERROR] Variant annotation error at 271631 2L_271631! Expected reference TTTT found gggt
      java.lang.RuntimeException: Variant annotation error at 271631 2L_271631! Expected reference TTTT found gggt
      at barna.astalavista.Scorer.scoreVariants(Scorer.java:504)
      at barna.astalavista.Scorer.scoreSites(Scorer.java:1044)
      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)

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            Assignee:
            micha Micha Sammeth
            Reporter:
            micha Micha Sammeth
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              Dates

              Created:
              Updated: