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Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3651 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-28 13:28:37 +00:00
parent 464ac63a22
commit bf5cbad04c
2 changed files with 18 additions and 6 deletions
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18
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -32,8 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
@ -49,7 +48,10 @@ import java.util.ArrayList;
* Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 and MQ0 reads.
*/
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.Event, RealignerTargetCreator.Event> {
@Reference(window=@Window(start=-1,stop=50))
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@By(DataSource.REFERENCE)
public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Event, RealignerTargetCreator.Event> {
// mismatch/entropy/SNP arguments
@Argument(fullName="windowSize", shortName="window", doc="window size for calculating entropy or SNP clusters", required=false)
@ -86,7 +88,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
long furthestStopPos = -1;
// look for insertions in the extended context (we'll get deletions from the normal context)
if ( context.hasExtendedEventPileup() ) {
if ( context != null && context.hasExtendedEventPileup() ) {
ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup();
if ( pileup.getNumberOfInsertions() > 0 ) {
hasIndel = hasInsertion = true;
@ -115,7 +117,9 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
hasInsertion = true;
break;
}
}
if ( hasIndel )
furthestStopPos = vc.getLocation().getStop();
}
}
// look at the normal context to get deletions and positions with high entropy
@ -154,13 +158,15 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
if ( !hasIndel && !hasPointEvent )
return null;
// return null if we didn't find any usable reads associated with the event
// return null if we didn't find any usable reads/rods associated with the event
if ( furthestStopPos == -1 )
return null;
GenomeLoc eventLoc = context.getLocation();
if ( hasInsertion )
eventLoc = GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), eventLoc.getStart()+1);
else if ( hasIndel && context.getBasePileup().size() == 0 )
eventLoc = GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), furthestStopPos);
EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT);

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -20,5 +20,11 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
1,
Arrays.asList("bfccfa50f62d10ee2fe8cfa68fb70002"));
executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf -BTI indels -o %s",
1,
Arrays.asList("1a11cfc9cc713617c82bdec503ebe02a"));
executeTest("test rods only", spec3);
}
}