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This along with Mauricio's previous commit (thanks!) fixes GSA-522. There are no longer any modifications to reads in the map calls of ActiveRegion walkers. Added the bam which identified this error as a new integration test.

This commit is contained in:
Ryan Poplin 2012-08-30 09:07:36 -04:00
parent 4d38befe86
commit 35baf0b155
3 changed files with 16 additions and 9 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -66,4 +66,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testHaplotypeCallerSingleSampleIndelQualityScores() { public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "e1f88fac91424740c0eaac1de48b3970"); HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "e1f88fac91424740c0eaac1de48b3970");
} }
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("000fd36d5cf8090386bb2ac15e3ab0b5"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
} }

1
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -241,6 +241,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
} }
} }
reads.removeAll( placedReads ); // remove all the reads which have been placed into their active region reads.removeAll( placedReads ); // remove all the reads which have been placed into their active region
// WARNING: This hashset relies on reads being exactly equal when they are placed in the list as when they are removed. So the ActiveRegionWalker can't modify the reads in any way.
logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc()); logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc());
final M x = walker.map( activeRegion, null ); final M x = walker.map( activeRegion, null );

16
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -228,8 +228,7 @@ public class GATKSAMRecord extends BAMRecord {
if( quals == null ) { if( quals == null ) {
quals = new byte[getBaseQualities().length]; quals = new byte[getBaseQualities().length];
Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
// be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45 // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
setBaseQualities(quals, EventType.BASE_INSERTION);
} }
return quals; return quals;
} }
@ -246,7 +245,6 @@ public class GATKSAMRecord extends BAMRecord {
quals = new byte[getBaseQualities().length]; quals = new byte[getBaseQualities().length];
Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will Arrays.fill(quals, (byte) 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
// be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45 // be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
setBaseQualities(quals, EventType.BASE_DELETION);
} }
return quals; return quals;
} }
@ -262,7 +260,7 @@ public class GATKSAMRecord extends BAMRecord {
public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) { public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
mReadGroup = readGroup; mReadGroup = readGroup;
retrievedReadGroup = true; retrievedReadGroup = true;
setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils! setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!
} }
/////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////
@ -367,15 +365,15 @@ public class GATKSAMRecord extends BAMRecord {
* Clears all attributes except ReadGroup of the read. * Clears all attributes except ReadGroup of the read.
*/ */
public GATKSAMRecord simplify () { public GATKSAMRecord simplify () {
GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities(); byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();
byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES) == null) ? null : getBaseDeletionQualities(); byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES) == null) ? null : getBaseDeletionQualities();
this.clearAttributes(); // clear all attributes from the read this.clearAttributes(); // clear all attributes from the read
this.setReadGroup(rg); // restore read group this.setReadGroup(rg); // restore read group
if (insQuals != null) if (insQuals != null)
this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
if (delQuals != null) if (delQuals != null)
this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any
return this; return this;
} }