From 4a451949baef72a93c8cc08db911e4cf84342add Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Jun 2010 22:13:25 +0000
Subject: [PATCH] add parallel option to target creator for masking out reads
 with bad mates

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3663 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java | 8 +++++++-
 .../indels/RealignerTargetCreatorIntegrationTest.java     | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index b127ff7b0..03fd5522b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -67,6 +67,9 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
     @Argument(fullName="maxIntervalSize", shortName="maxInterval", doc="maximum interval size", required=false)
     protected int maxIntervalSize = 500;
 
+    @Argument(fullName="realignReadsWithBadMates", required=false, doc="Should we try to realign paired-end reads whose mates map to other chromosomes?")
+    protected boolean REALIGN_BADLY_MATED_READS = false;
+
     @Override
     public boolean generateExtendedEvents() { return true; }
 
@@ -129,8 +132,11 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
             int mismatchQualities = 0, totalQualities = 0;
             byte refBase = ref.getBase();
             for (PileupElement p : pileup ) {
-                // check the ends of the reads to see how far they extend
                 SAMRecord read = p.getRead();
+                if ( !REALIGN_BADLY_MATED_READS && read.getReadPairedFlag() && !read.getMateUnmappedFlag() && read.getMateReferenceIndex() != read.getReferenceIndex() )
+                    continue;
+
+                // check the ends of the reads to see how far they extend
                 furthestStopPos = Math.max(furthestStopPos, read.getAlignmentEnd());
 
                 // is it a deletion? (sanity check in case extended event missed it)
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index f1b338789..0a543967a 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -10,13 +10,13 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
     public void testIntervals() {
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
+                "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
                  1,
                  Arrays.asList("d21e83a8b0d3f63acd9ca3b0b636e515"));
         executeTest("test standard", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
+                "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
                  1,
                  Arrays.asList("bfccfa50f62d10ee2fe8cfa68fb70002"));
         executeTest("test dbsnp", spec2);