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Merged bug fix from Stable into Unstable

This commit is contained in:
Matt Hanna 2012-01-12 13:31:10 -05:00
parent ed34b4f088 cd43f016ce
commit 2c3176eb80
2 changed files with 23 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
View File

@ -256,7 +256,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
// Naive algorithm: find all elements in current contig for proper schedule creation.
List<GenomeLoc> lociInContig = new LinkedList<GenomeLoc>();
for(GenomeLoc locus: loci) {
if(dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded)
if(!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded)
lociInContig.add(locus);
}

22
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -83,6 +83,28 @@ public class IntervalIntegrationTest extends WalkerTest {
executeTest("testUnmappedReadInclusion",spec);
}
@Test
public void testMixedMappedAndUnmapped() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads" +
" -I " + validationDataLocation + "MV1994.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -L Escherichia_coli_K12:4630000-4639675" +
" -L unmapped" +
" -U",
0, // two output files
Collections.<String>emptyList());
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("083ef1e9ded868e0d12c05a1354c0319",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);
}
@Test(enabled = false)
public void testUnmappedReadExclusion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(