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Trivial output changes for consistency 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-07 14:47:43 +00:00
parent 058e7d3d12
commit e7dad728df
2 changed files with 4 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -141,11 +141,11 @@ public class VariantAnnotatorEngine {
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations )
descriptions.add(annotation.getDescription()); descriptions.add(annotation.getDescription());
if ( annotateDbsnp ) if ( annotateDbsnp )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP membership")); descriptions.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP Membership"));
if ( annotateHapmap2 ) if ( annotateHapmap2 )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 2 membership")); descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 2 Membership"));
if ( annotateHapmap3 ) if ( annotateHapmap3 )
descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 3 membership")); descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 3 Membership"));
return descriptions; return descriptions;
} }

1
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -587,6 +587,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} catch (Exception e) {} } catch (Exception e) {}
} }
} else { } else {
//System.out.println("CLEAN: " + AlignmentUtils.cigarToString(bestConsensus.cigar) + " " + bestConsensus.str.toString() + " " + bestConsensus.cigar.numCigarElements() );
//logger.debug("CLEAN: " + AlignmentUtils.cigarToString(bestConsensus.cigar) + " " + bestConsensus.str ); //logger.debug("CLEAN: " + AlignmentUtils.cigarToString(bestConsensus.cigar) + " " + bestConsensus.str );
if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) { if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
// NOTE: indels are printed out in the format specified for the low-coverage pilot1 // NOTE: indels are printed out in the format specified for the low-coverage pilot1