From 01ffa307c21b7ba6835a276424480073fc2b217e Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 16 Jun 2010 19:36:36 +0000 Subject: [PATCH] When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3569 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 2 +- .../gatk/walkers/indels/IndelRealignerIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index dcb87b79a..705dcdad7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -183,7 +183,7 @@ public class IndelRealigner extends ReadWalker { List ids = getToolkit().getDataSource().getReaderIDs(); for ( SAMReaderID id: ids ) { File file = getToolkit().getDataSource().getSAMFile(id); - SAMFileHeader header = getToolkit().getSAMFileHeader(id); + SAMFileHeader header = getToolkit().getSAMFileHeader(); String newFileName = file.getName().substring(0, file.getName().length()-3) + outputSuffix + ".bam"; File newFile = new File(baseWriterFilename, newFileName); SAMFileWriter writer = makeWriter(factory, header, newFile); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 5f3b795f7..56107c997 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -32,10 +32,10 @@ public class IndelRealignerIntegrationTest extends WalkerTest { Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3")); File file1 = new File("/tmp/" + filename1 + ".cleaned.bam"); file1.deleteOnExit(); - spec3.addAuxFile("7e1c5a74e572c3e0fbc14f98021e04b4", file1); + spec3.addAuxFile("1ceae553c8aa20681ed0736d4d2b4541", file1); File file2 = new File("/tmp/" + filename2 + ".cleaned.bam"); file2.deleteOnExit(); - spec3.addAuxFile("7a796195c3f13a3c84cd7209f3030d85", file2); + spec3.addAuxFile("ce8ddeae5a5aab836ac1dde9448ccb66", file2); executeTest("test NWay", spec3); } } \ No newline at end of file