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Fix Picard OTF index generation issue. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5077 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-01-26 03:42:46 +00:00
parent ce5b11317b
commit 862b299b47
1 changed files with 16 additions and 0 deletions
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16
java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -443,4 +443,20 @@ public class GATKSAMRecord extends SAMRecord {
public String toString() { return mRecord.toString(); } public String toString() { return mRecord.toString(); }
public SAMFileSource getFileSource() { return mRecord.getFileSource(); } public SAMFileSource getFileSource() { return mRecord.getFileSource(); }
/**
* Sets a marker providing the source reader for this file and the position in the file from which the read originated.
* @param fileSource source of the given file.
*/
@Override
protected void setFileSource(final SAMFileSource fileSource) {
try {
Method method = SAMRecord.class.getDeclaredMethod("setFileSource",SAMFileSource.class);
method.setAccessible(true);
method.invoke(mRecord,fileSource);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setFileSource method",ex);
}
}
} }