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Fixing an off-by-one clipping error in ReduceReads for reads off the contig 

Reads that are soft-clipped off the contig (before the beginning of the contig) were being soft-clipped to position 0 instead of 1 because of an off-by-one issue. Fixed and included in the integration test.
This commit is contained in:
Mauricio Carneiro 2012-12-13 21:56:44 -05:00
parent 74344a3871
commit 5f1afb4136
2 changed files with 2 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -300,7 +300,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
// Check if the read goes beyond the boundaries of the chromosome, and hard clip those boundaries.
int chromosomeLength = ref.getGenomeLocParser().getContigInfo(read.getReferenceName()).getSequenceLength();
if (read.getSoftStart() < 0)
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart() - 1);
read = ReadClipper.hardClipByReadCoordinates(read, 0, -read.getSoftStart());
if (read.getSoftEnd() > chromosomeLength)
read = ReadClipper.hardClipByReadCoordinates(read, chromosomeLength - read.getSoftStart() + 1, read.getReadLength() - 1);

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
View File

@ -94,7 +94,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testReadOffContig() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, OFFCONTIG_BAM) + " -o %s ";
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("53e16367d333da0b7d40a7683a35c95f")));
executeTest("testReadOffContig", new WalkerTestSpec(base, Arrays.asList("2f17c1a78e9d0138217fdb83cede8f68")));
}
}