zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

In retrospect, it wasn't a good idea to have FisherStrand handle reduced reads since they are always on the forward strand. For now, FS ignores reduced reads but I've added a note (and JIRA) to make this work once the RR het compression is enabled (since we will have directionality in reads then).

This commit is contained in:
Eric Banks 2012-12-05 02:00:35 -05:00
parent 726332db79
commit ef87b18e09
2 changed files with 7 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -457,7 +457,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testReducedBamSNPs() {
testReducedCalling("SNP", "f5ccbc96d0d66832dd9b3c5cb6507db4");
testReducedCalling("SNP", "dee6590e3b7079890bc3a9cb372c297e");
}
@Test

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -276,6 +276,12 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {
// ignore reduced reads because they are always on the forward strand!
// TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test
if ( p.getRead().isReducedRead() )
continue;
if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions
continue;