From dc292c0317a891a48f34016e3b2d33fb8d4d884f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 9 Jul 2012 14:27:01 -0700 Subject: [PATCH] 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. --- .../src/org/broadinstitute/sting/gatk/filters/ReadFilter.java | 1 + .../sting/gatk/walkers/annotator/FisherStrand.java | 3 --- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index 641bddb2d..d8caa3dea 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -28,6 +28,7 @@ public abstract class ReadFilter implements SamRecordFilter { * @return true if the SAMRecords matches the filter, otherwise false * @throws UnsupportedOperationException when paired filter not implemented */ + @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) { throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass()); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index e3ee8c923..e3b9761fb 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -258,9 +258,6 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat if ( p.isDeletion() || p.getRead().isReducedRead() ) // ignore deletions and reduced reads continue; - if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 ) - continue; // todo -- fixme, should take filtered context! - Allele base = Allele.create(p.getBase(), false); boolean isFW = !p.getRead().getReadNegativeStrandFlag();