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Fix SV QNameFinder to handle reads with negative unclipped starts #5864

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merged 1 commit into from
Apr 6, 2019
Merged

Fix SV QNameFinder to handle reads with negative unclipped starts #5864

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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/QNameFinder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@ public Iterator<QNameAndInterval> apply( final GATKRead read ) {
}
if ( intervalsIndex >= intervalsSize ) return noName;
final SVInterval indexedInterval = intervals.get(intervalsIndex);
final SVInterval unclippedReadInterval = new SVInterval(readContigId, read.getUnclippedStart(), read.getUnclippedEnd());
final SVInterval unclippedReadInterval = new SVInterval(readContigId,
Math.max(0, read.getUnclippedStart()), read.getUnclippedEnd());
if ( indexedInterval.isDisjointFrom(unclippedReadInterval) ) return noName;
final SVInterval clippedReadInterval = new SVInterval(readContigId, read.getStart(), read.getEnd());
if (filter.containedInRegionToIgnore(clippedReadInterval, highCoverageSubIntervals)) return noName;
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32 changes: 32 additions & 0 deletions src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/QNameFinderTest.java
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Expand Up @@ -59,4 +59,36 @@ public void testHighDepthRegionFiltering() throws Exception {

}

@Test
public void testReadWithNegativeUnclippedStart() throws Exception {
final StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection params =
new StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection();
final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeaderWithGroups(3, 1, 10000000, 1);
final Set<Integer> crossContigIgnoreSet = new HashSet<>();
final ReadMetadata readMetadata = new ReadMetadata(crossContigIgnoreSet, header, LIBRARY_STATISTICS, null, 2L, 2L, 1);
final ArrayList<SVInterval> intervals = new ArrayList<>(2);
SVInterval interval1 = new SVInterval(0, 25, 125);
intervals.add(interval1);
final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1,
ArtificialReadUtils.createRandomReadBases(151, false),
ArtificialReadUtils.createRandomReadQuals(151),
"50S101M");
read1.setIsReverseStrand(true);
final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, "read2", 0, 130,
ArtificialReadUtils.createRandomReadBases(151, false),
ArtificialReadUtils.createRandomReadQuals(151),
"40S111M");

final SVIntervalTree<SVInterval> highDepthIntervals = new SVIntervalTree<>();

final QNameFinder qNameFinder = new QNameFinder(readMetadata, intervals, new SVReadFilter(params), highDepthIntervals);

Iterator<QNameAndInterval> read1Result = qNameFinder.apply(read1);
Assert.assertTrue( read1Result.hasNext());

Iterator<QNameAndInterval> read2Result = qNameFinder.apply(read2);
Assert.assertFalse( read2Result.hasNext());

}

}