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Fixes GSA-558 GATK ReadShards don't handle unmapped reads correctly.

This commit is contained in:
Mark DePristo 2012-09-10 16:39:49 -04:00
parent 641c6a361e
commit d6e42d839c
1 changed files with 10 additions and 2 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
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@ -8,7 +8,10 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*; import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
/** /**
* *
@ -149,7 +152,12 @@ public class ReadShard extends Shard {
if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd(); if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd();
} }
return parser.createGenomeLoc(contig, start, stop); assert contig != null;
if ( contig.equals("*") ) // all reads are unmapped
return GenomeLoc.UNMAPPED;
else
return parser.createGenomeLoc(contig, start, stop);
} }
} }
} }