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FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations 

-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.
This commit is contained in:
Mark DePristo 2012-07-09 14:27:01 -07:00
parent bd799fc989
commit dc292c0317
2 changed files with 1 additions and 3 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
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@ -28,6 +28,7 @@ public abstract class ReadFilter implements SamRecordFilter {
* @return true if the SAMRecords matches the filter, otherwise false * @return true if the SAMRecords matches the filter, otherwise false
* @throws UnsupportedOperationException when paired filter not implemented * @throws UnsupportedOperationException when paired filter not implemented
*/ */
@Override
public boolean filterOut(final SAMRecord first, final SAMRecord second) { public boolean filterOut(final SAMRecord first, final SAMRecord second) {
throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass()); throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass());
} }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -258,9 +258,6 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
continue; continue;
if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 )
continue; // todo -- fixme, should take filtered context!
Allele base = Allele.create(p.getBase(), false); Allele base = Allele.create(p.getBase(), false);
boolean isFW = !p.getRead().getReadNegativeStrandFlag(); boolean isFW = !p.getRead().getReadNegativeStrandFlag();