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Missorted BAMs are User Exceptions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5080 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-26 14:09:39 +00:00
parent be697d96f9
commit 01e032e89c
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
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@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.iterators; package org.broadinstitute.sting.gatk.iterators;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.RuntimeIOException;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.Iterator; import java.util.Iterator;
@ -35,7 +35,7 @@ public class VerifyingSamIterator implements StingSAMIterator {
private void verifyRecord( final SAMRecord last, final SAMRecord cur ) { private void verifyRecord( final SAMRecord last, final SAMRecord cur ) {
if ( checkOrderP && isOutOfOrder(last, cur) ) { if ( checkOrderP && isOutOfOrder(last, cur) ) {
this.last = null; this.last = null;
throw new RuntimeIOException(String.format("Reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()) ); throw new UserException.MissortedBAM(String.format("reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()) );
} }
} }