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one trivial walker to filter reads; bam in -> filter -> bam out 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@478 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-21 20:39:29 +00:00
parent 61e855200d
commit ece3e9969e
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers;
import java.io.File; import java.io.File;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory; import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
@ -25,7 +26,7 @@ public class ReadFilterWalker extends ReadWalker<Integer,Integer> {
@Override @Override
public Integer map(LocusContext context, SAMRecord read) { public Integer map(LocusContext context, SAMRecord read) {
if ( writer == null ) writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(read.getHeader(), true, new File(output)); if ( writer == null ) writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(read.getHeader(), read.getHeader().getSortOrder() != SAMFileHeader.SortOrder.unsorted, new File(output));
writer.addAlignment(read); writer.addAlignment(read);
return 1; return 1;
} }