Changeset 5998


Ignore:
Timestamp:
Sep 9, 2020, 9:07:58 AM (12 months ago)
Author:
Nicklas Nordborg
Message:

Merge Reggie 4.27.2 to the trunk. Seems like this was missed when Reggie 4.27.2 was released (#5966).

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk

  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

    r5973 r5998  
    19791979  {
    19801980    if (m.getAnnotationTypeNameScores() == null) return null;
    1981     return new Annotationtype(m.getAnnotationTypeNameScores(), Type.STRING, false, m.getDescription(), Item.RAWBIOASSAY);
     1981    return new Annotationtype(m.getAnnotationTypeNameScores(), Type.TEXT, false, m.getDescription(), Item.RAWBIOASSAY);
    19821982  }
    19831983 
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

    r5930 r5998  
    255255      File bamFile = Datafiletype.BAM.getFile(dc, aligned);
    256256     
    257       String libName = ScriptUtil.checkValidScriptParameter(lib.getName());
     257      String alignedName = ScriptUtil.checkValidScriptParameter(aligned.getName());
    258258      if (specimen != null && specimen.getExternalId() != null)
    259259      {
    260         // Replace SCANB-ID in libName with Sample.externalId
    261         libName = libName.replace(specimen.getName(), specimen.getExternalId());
     260        // Replace SCANB-ID in alignedName with Sample.externalId
     261        alignedName = alignedName.replace(specimen.getName(), specimen.getExternalId());
    262262      }
    263263     
     
    405405        vardictCmd += " | ${VarDictPath}/bin/teststrandbias.R";
    406406        vardictCmd += " | ${VarDictPath}/bin/var2vcf_valid.pl";
    407         vardictCmd += " -N " + libName;
     407        vardictCmd += " -N " + alignedName;
    408408        vardictCmd += " " + var2vcf_options;
    409409        vardictCmd += " > tmp/variants-raw-1.vcf";
     
    478478        script.cmd("if [ $NUMFILTERED -gt 0 ]; then");
    479479        String mutSignCmd = "./Rscript.sh ./mutation_signature.R";
    480         mutSignCmd += " " + libName;
     480        mutSignCmd += " " + alignedName;
    481481        mutSignCmd += " resultsfilter/variants-filtered.vcf";
    482482        mutSignCmd += " " + cosmic_signatures_path;
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