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Added code to extend Matt's getReferenceBases out to the read walkers, so they can see the corresponding reference for each read. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@652 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-05-11 03:42:38 +00:00
parent 4ce3feba4d
commit e8b8ab5985
2 changed files with 16 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ShardDataProvider.java
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import net.sf.samtools.SAMRecord;
/** /**
* User: hanna * User: hanna
* Date: May 8, 2009 * Date: May 8, 2009
@ -107,6 +108,15 @@ public class ShardDataProvider {
return referenceProvider.getReferenceBase(genomeLoc); return referenceProvider.getReferenceBase(genomeLoc);
} }
/**
* Gets the reference base associated with this particular point on the genome.
* @param read the read to fetch the reference sequence for
* @return a char string of bases representing the reference sequence corresponding to passed in read
*/
public char[] getReferenceForRead( SAMRecord read ) {
return referenceProvider.getReferenceBases(read);
}
/** /**
* Create a data provider for the shard given the reads and reference. * Create a data provider for the shard given the reads and reference.
* @param shard The chunk of data over which traversals happen. * @param shard The chunk of data over which traversals happen.

11
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -95,21 +95,23 @@ public class TraverseReads extends TraversalEngine {
// our locus context // our locus context
LocusContext locus = null; LocusContext locus = null;
// an array of characters that represent the reference
char[] refSeq = null;
if (read.getReferenceIndex() >= 0) { if (read.getReferenceIndex() >= 0) {
// get the genome loc from the read // get the genome loc from the read
GenomeLoc site = new GenomeLoc(read); GenomeLoc site = new GenomeLoc(read);
// Jump forward in the reference to this locus location // Jump forward in the reference to this locus location
locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0)); locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));
// get the array of characters for the reference sequence, since we're a mapped read
refSeq = dataProvider.getReferenceForRead( read );
} }
// update the number of reads we've seen // update the number of reads we've seen
TraversalStatistics.nRecords++; TraversalStatistics.nRecords++;
// we still have to fix the locus context provider to take care of this problem with > 1 length contexts
// LocusContext locus = locusProvider.getLocusContext(site);
final boolean keepMeP = readWalker.filter(locus, read); final boolean keepMeP = readWalker.filter(locus, read);
if (keepMeP) { if (keepMeP) {
M x = readWalker.map(locus, read); M x = readWalker.map(locus, read);
@ -118,7 +120,6 @@ public class TraverseReads extends TraversalEngine {
if (locus != null) { printProgress("loci", locus.getLocation()); } if (locus != null) { printProgress("loci", locus.getLocation()); }
} }
//System.err.println(TraversalStatistics.nRecords);
return sum; return sum;
} }