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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
This commit is contained in:
ebanks 2010-06-16 19:36:36 +00:00
parent 05c2f96bb4
commit 01ffa307c2
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -183,7 +183,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
List<SAMReaderID> ids = getToolkit().getDataSource().getReaderIDs(); List<SAMReaderID> ids = getToolkit().getDataSource().getReaderIDs();
for ( SAMReaderID id: ids ) { for ( SAMReaderID id: ids ) {
File file = getToolkit().getDataSource().getSAMFile(id); 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"; String newFileName = file.getName().substring(0, file.getName().length()-3) + outputSuffix + ".bam";
File newFile = new File(baseWriterFilename, newFileName); File newFile = new File(baseWriterFilename, newFileName);
SAMFileWriter writer = makeWriter(factory, header, newFile); SAMFileWriter writer = makeWriter(factory, header, newFile);

4
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -32,10 +32,10 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3")); Arrays.asList("bd42a4fa66d7ec7a480c2b94313a78d3"));
File file1 = new File("/tmp/" + filename1 + ".cleaned.bam"); File file1 = new File("/tmp/" + filename1 + ".cleaned.bam");
file1.deleteOnExit(); file1.deleteOnExit();
spec3.addAuxFile("7e1c5a74e572c3e0fbc14f98021e04b4", file1); spec3.addAuxFile("1ceae553c8aa20681ed0736d4d2b4541", file1);
File file2 = new File("/tmp/" + filename2 + ".cleaned.bam"); File file2 = new File("/tmp/" + filename2 + ".cleaned.bam");
file2.deleteOnExit(); file2.deleteOnExit();
spec3.addAuxFile("7a796195c3f13a3c84cd7209f3030d85", file2); spec3.addAuxFile("ce8ddeae5a5aab836ac1dde9448ccb66", file2);
executeTest("test NWay", spec3); executeTest("test NWay", spec3);
} }
} }