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Simplify handling of reference sequence for unmapped reads. Improvement made based on a suggestion from Alec. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2475 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-29 21:06:20 +00:00
parent 96c4929b3c
commit 05deb8796b
1 changed files with 3 additions and 19 deletions
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22
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView; import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView; import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
@ -13,11 +12,8 @@ import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.Arrays;
/* /*
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
* *
@ -96,24 +92,12 @@ public class TraverseReads extends TraversalEngine {
// while we still have more reads // while we still have more reads
for (SAMRecord read : reads) { for (SAMRecord read : reads) {
// our locus context
AlignmentContext locus = null;
// an array of characters that represent the reference // an array of characters that represent the reference
char[] refSeq = null; char[] refSeq = null;
if (needsReferenceBasesP && read.getReferenceIndex() >= 0) { // get the array of characters for the reference sequence, since we're a mapped read
// get the genome loc from the read if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
GenomeLoc site = GenomeLocParser.createGenomeLoc(read); refSeq = reference.getReferenceBases(read);
// Jump forward in the reference to this locus location
locus = new AlignmentContext(site, Arrays.asList(read), Arrays.asList(0));
// get the array of characters for the reference sequence, since we're a mapped read
if( dataProvider.hasReference() )
refSeq = reference.getReferenceBases( read );
}
// update the number of reads we've seen // update the number of reads we've seen
TraversalStatistics.nRecords++; TraversalStatistics.nRecords++;