From ece3e9969e1bd384f100f37ec42c0cc8bb371189 Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 21 Apr 2009 20:39:29 +0000 Subject: [PATCH] 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 --- .../sting/playground/gatk/walkers/ReadFilterWalker.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java index c3f7b30ec..0d29bce08 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java @@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.gatk.walkers; import java.io.File; +import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriterFactory; import net.sf.samtools.SAMRecord; @@ -25,7 +26,7 @@ public class ReadFilterWalker extends ReadWalker { @Override 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); return 1; }