From ef87b18e09d64dda2e483c77573b792af46d4f93 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 5 Dec 2012 02:00:35 -0500 Subject: [PATCH] In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then). --- .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 2 +- .../sting/gatk/walkers/annotator/FisherStrand.java | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 9f940dce5..9e9c7e37e 100755 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -457,7 +457,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testReducedBamSNPs() { - testReducedCalling("SNP", "f5ccbc96d0d66832dd9b3c5cb6507db4"); + testReducedCalling("SNP", "dee6590e3b7079890bc3a9cb372c297e"); } @Test 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 bdf7baec9..52072d10c 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 @@ -276,6 +276,12 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat for ( Map.Entry sample : stratifiedContexts.entrySet() ) { for (PileupElement p : sample.getValue().getBasePileup()) { + + // ignore reduced reads because they are always on the forward strand! + // TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test + if ( p.getRead().isReducedRead() ) + continue; + if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions continue;