zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Make sure compression level always gets pushed into SAMFileWriterFactory. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1699 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-23 18:20:26 +00:00
parent fa87dd386d
commit ebfbe56b43
1 changed files with 1 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
View File

@ -31,7 +31,6 @@ import net.sf.samtools.util.CloseableIterator;
import java.io.*; import java.io.*;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
import org.broadinstitute.sting.gatk.io.storage.Storage;
/** /**
* Provides temporary storage for SAMFileWriters. * Provides temporary storage for SAMFileWriters.
@ -49,7 +48,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) { public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
this.file = file; this.file = file;
this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file ); this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
} }
public void addAlignment( SAMRecord read ) { public void addAlignment( SAMRecord read ) {