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Expose the underlying SAM reader to the walkers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@270 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-02 21:38:00 +00:00
parent 8ce4dabd7c
commit b7a67da775
2 changed files with 5 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk;
import edu.mit.broad.picard.reference.ReferenceSequence; import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.reference.ReferenceSequenceFile; import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory; import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency; import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
@ -395,4 +396,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName()))); contig.getName(), refFile.getDistanceBetweenContigs("chr1", contig.getName())));
} }
} }
public SAMFileReader getSamReader() { return this.engine.getSamReader(); }
} }

2
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -538,4 +538,6 @@ public abstract class TraversalEngine {
logger.warn(msg); logger.warn(msg);
} }
} }
public SAMFileReader getSamReader() { return this.samReader; }
} }