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

Update TODO list

This commit is contained in:
Joel Thibault 2012-12-05 12:45:02 -05:00
parent abd94b2976
commit cc4e3ec589
1 changed files with 6 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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

@ -109,6 +109,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
dictionary = reference.getSequenceDictionary(); dictionary = reference.getSequenceDictionary();
genomeLocParser = new GenomeLocParser(dictionary); genomeLocParser = new GenomeLocParser(dictionary);
// TODO: test shard boundaries
intervals = new ArrayList<GenomeLoc>(); intervals = new ArrayList<GenomeLoc>();
intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20)); intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20));
intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999)); intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999));
@ -139,8 +141,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
List<GenomeLoc> activeIntervals = getIsActiveIntervals(walker, intervals); List<GenomeLoc> activeIntervals = getIsActiveIntervals(walker, intervals);
// Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call // Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call
verifyEqualIntervals(intervals, activeIntervals); verifyEqualIntervals(intervals, activeIntervals);
// TODO: more tests and edge cases
} }
private List<GenomeLoc> getIsActiveIntervals(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) { private List<GenomeLoc> getIsActiveIntervals(DummyActiveRegionWalker walker, List<GenomeLoc> intervals) {
@ -171,8 +171,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values(); Collection<ActiveRegion> activeRegions = getActiveRegions(walker, intervals).values();
verifyActiveRegionCoverage(intervals, activeRegions); verifyActiveRegionCoverage(intervals, activeRegions);
// TODO: more tests and edge cases
} }
private void verifyActiveRegionCoverage(List<GenomeLoc> intervals, Collection<ActiveRegion> activeRegions) { private void verifyActiveRegionCoverage(List<GenomeLoc> intervals, Collection<ActiveRegion> activeRegions) {
@ -279,8 +277,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20"); getRead(region, "simple20");
// TODO: more tests and edge cases
} }
@Test @Test
@ -348,8 +344,6 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20"); getRead(region, "simple20");
// TODO: more tests and edge cases
} }
@Test @Test
@ -418,8 +412,11 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals"); verifyReadNotPlaced(region, "outside_intervals");
getRead(region, "simple20"); getRead(region, "simple20");
}
// TODO: more tests and edge cases @Test
public void testUnmappedReads() {
// TODO
} }
private void verifyReadNotPlaced(ActiveRegion region, String readName) { private void verifyReadNotPlaced(ActiveRegion region, String readName) {