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Let Picard specify the default compression level. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1701 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-23 19:01:48 +00:00
parent f783cb30e0
commit 856bbd0320
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -48,7 +48,10 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
this.file = file;
this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
if( stub.getCompressionLevel() != null )
this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
else
this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file );
}
public void addAlignment( SAMRecord read ) {