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Fix for reads that are all insertions (e.g. 50I) and causing the IndelRealigner to error out.

This commit is contained in:
Eric Banks 2014-03-21 15:01:34 -04:00
parent 69eaf7c82d
commit 32a96e3ab3
2 changed files with 3 additions and 2 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
View File

@ -81,7 +81,7 @@ class ReadBin implements HasGenomeLocation {
final int readStart = read.getSoftStart();
final int readStop = read.getSoftEnd();
if ( loc == null )
loc = parser.createGenomeLoc(read.getReferenceName(), readStart, readStop);
loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion
else if ( readStop > loc.getStop() )
loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop);

3
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBinUnitTest.java
View File

@ -81,6 +81,7 @@ public class ReadBinUnitTest {
{"20S80M", 80},
{"80M20S", 1},
{"20S60M20S", 50},
{"50I", 60},
{"100M", 500}
};
}
@ -94,7 +95,7 @@ public class ReadBinUnitTest {
@Test(enabled = true, dataProvider = "reads")
public void testAddingReads(String cigarString, int alignmentStart) {
final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart);
final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), read.getSoftEnd());
final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd()));
Assert.assertEquals(readBin.getLocation(), readLoc);
readBin.clear();
}