From a57295eb755ca3d9b838373eb7c7e54d2c5d72c3 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 20 Apr 2012 14:02:55 -0400 Subject: [PATCH] Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold). --- .../sting/utils/activeregion/ActivityProfile.java | 4 ++-- .../CountReadsInActiveRegionsIntegrationTest.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 6ef5a2af2..70593bbed 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -158,11 +158,11 @@ public class ActivityProfile { // find the best place to break up the large active region Double minProb = Double.MAX_VALUE; int cutPoint = -1; - for( int iii = curStart + 45; iii < curEnd - 45; iii++ ) { // BUGBUG: assumes maxRegionSize >> 45 + for( int iii = curStart + 50; iii < curEnd - 50; iii++ ) { // BUGBUG: assumes maxRegionSize >> 50 if( isActiveList.get(iii) < minProb ) { minProb = isActiveList.get(iii); cutPoint = iii; } } final List leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList()); - final List rightList = createActiveRegion(isActive, cutPoint, curEnd, activeRegionExtension, maxRegionSize, new ArrayList()); + final List rightList = createActiveRegion(isActive, cutPoint+1, curEnd, activeRegionExtension, maxRegionSize, new ArrayList()); returnList.addAll( leftList ); returnList.addAll( rightList ); return returnList; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java index 7d1fc637b..250a3d368 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java @@ -38,7 +38,7 @@ public class CountReadsInActiveRegionsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T CountReadsInActiveRegions -R " + b37KGReference + " -I " + b37GoodNA12878BAM + " -L 20:10,000,000-10,200,000 -o %s", 1, - Arrays.asList("1e9e8d637d2acde23fa99fe9dc07e3e2")); + Arrays.asList("942d067e6863a3f3524f67dc0aa02ef2")); executeTest("CountReadsInActiveRegions:", spec); } } \ No newline at end of file