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If alignment context at the locus holds extended event, get rod metadata and (importantly) reference bases for the whole span of the event (if it is a deletion that is, insertions still have length 0 on the ref!) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2489 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-30 21:56:25 +00:00
parent a41cb0701b
commit a18e31f5b8
1 changed files with 14 additions and 3 deletions
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17
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -12,6 +12,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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.GenomeLoc;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.ArrayList; import java.util.ArrayList;
@ -66,13 +67,23 @@ public class TraverseLoci extends TraversalEngine {
// We keep processing while the next reference location is within the interval // We keep processing while the next reference location is within the interval
while( locusView.hasNext() ) { while( locusView.hasNext() ) {
AlignmentContext locus = locusView.next(); AlignmentContext locus = locusView.next();
GenomeLoc location = locus.getLocation();
TraversalStatistics.nRecords++; TraversalStatistics.nRecords++;
// Iterate forward to get all reference ordered data covering this locus if ( locus.hasExtendedEventPileup() ) {
final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation()); // if the alignment context we received holds an "extended" pileup (i.e. pileup of insertions/deletions
// associated with the current site), we need to update the location. The updated location still starts
// at the current genomic position, but it has to span the length of the longest deletion (if any).
location = GenomeLocParser.setStop(location,location.getStop()+locus.getExtendedEventPileup().getMaxDeletionLength());
}
ReferenceContext refContext = referenceView.getReferenceContext(locus.getLocation()); // Iterate forward to get all reference ordered data covering this location
final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(location);
// create reference context. Note that if we have a pileup of "extended events", the context will
// hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup).
ReferenceContext refContext = referenceView.getReferenceContext(location);
final boolean keepMeP = locusWalker.filter(tracker, refContext, locus); final boolean keepMeP = locusWalker.filter(tracker, refContext, locus);
if (keepMeP) { if (keepMeP) {