Changeset 5776


Ignore:
Timestamp:
Dec 6, 2019, 8:07:51 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1210: Variant calling fails if no variants are found

Updated the manual confirmation wizard so that 0 variants is not considered an error condition.

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

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/vcall_confirm.js

    r5730 r5776  
    7878     
    7979      var vcallJob = raw.vcallJob;
    80       var isError = !raw.vcfFile || !raw.spots;
     80      var isError = !raw.vcfFile || raw.VariantsPassedFilter == null;
    8181      var flagChecked = false;
    8282 
     
    9999      if (raw.vcfFile)
    100100      {
    101         html += raw.spots + '<span class="link vcf-link" data-file-id="'+raw.vcfFile.id+'" data-item-id="'+raw.id+'" title="View summary for the variants"><img src="../images/vcf_file.png" style="margin-left: 2px;"></span>';
     101        html += raw.VariantsPassedFilter + '<span class="link vcf-link" data-file-id="'+raw.vcfFile.id+'" data-item-id="'+raw.id+'" title="View summary for the variants"><img src="../images/vcf_file.png" style="margin-left: 2px;"></span>';
    102102      }
    103103      html += '</td>';
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java

    r5766 r5776  
    172172        {
    173173          RawBioAssay rba = raw.getItem();
    174           raw.setAnnotation("spots", rba.getNumFileSpots());
    175174          raw.loadAnnotations(dc, manager, "DataFilesFolder", Annotationtype.DATA_FILES_FOLDER, null);
     175          raw.loadAnnotations(dc, manager, "VariantsPassedFilter", Annotationtype.VARIANTS_PASSED_FILTER, null);
    176176         
    177177          DerivedBioAssay alignment = rba.getParentBioAssay();
     178          raw.setAnnotation("CallableBases", Annotationtype.CALLABLE_BASES.getAnnotationValue(dc, manager, alignment));
    178179          raw.setAnnotation("VariantsRaw", Annotationtype.VARIANTS_RAW.getAnnotationValue(dc, manager, alignment));
    179           raw.setAnnotation("CallableBases", Annotationtype.CALLABLE_BASES.getAnnotationValue(dc, manager, alignment));
    180180         
    181181          File vcf = raw.getFile(dc, Datafiletype.VCF);
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