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

Active Region extensions must stay on contig

This commit is contained in:
Joel Thibault 2013-01-02 13:46:33 -05:00
parent 09199366b7
commit dcb7735d3c
1 changed files with 15 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java
View File

@ -241,6 +241,21 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
Assert.assertEquals(intervalStops.size(), 0, "Interval stop location does not match an active region stop location");
}
@Test
public void testActiveRegionExtensionOnContig() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker();
Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values();
for (ActiveRegion activeRegion : activeRegions) {
GenomeLoc loc = activeRegion.getExtendedLoc();
// Contract: active region extensions must stay on the contig
Assert.assertTrue(loc.getStart() > 0, "Active region extension begins at location " + loc.getStart() + ", past the left end of the contig");
int refLen = dictionary.getSequence(loc.getContigIndex()).getSequenceLength();
Assert.assertTrue(loc.getStop() <= refLen, "Active region extension ends at location " + loc.getStop() + ", past the right end of the contig");
}
}
@Test
public void testPrimaryReadMapping() {
DummyActiveRegionWalker walker = new DummyActiveRegionWalker();