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Add a read and interval on a different contig

This commit is contained in:
Joel Thibault 2012-11-26 11:48:05 -05:00
parent 9531e58445
commit cc550b4145
1 changed files with 20 additions and 7 deletions
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27
public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
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@ -96,8 +96,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999));
intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999));
intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000));
// TODO: this fails!
//intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 20000));
intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100));
intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList();
reads = new ArrayList<SAMRecord>();
@ -109,8 +108,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
reads.add(buildSAMRecord("extended_only", "1", 3000, 3100));
reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990));
reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000));
// TODO
//reads.add(buildSAMRecord("simple20", "20", 10100, 10150));
reads.add(buildSAMRecord("simple20", "20", 10025, 10075));
}
@Test
@ -204,9 +202,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
// extended_only: Extended in 1:2000-2999
// extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999
// outside_intervals: none
// TODO
// simple20: Primary in 20:10000-20000
// simple20: Primary in 20:10000-10100
Map<GenomeLoc, ActiveRegion> activeRegions = getActiveRegions(walker, intervals);
ActiveRegion region;
@ -221,6 +217,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "extended_only");
// TODO: fail verifyReadNonPrimary(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999));
@ -232,6 +229,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
verifyReadNotPlaced(region, "extended_only");
// TODO: fail verifyReadPrimary(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999));
@ -243,6 +241,19 @@ public class TraverseActiveRegionsTest extends BaseTest {
// TODO: fail verifyReadExtended(region, "extended_only");
// TODO: fail verifyReadExtended(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadNotPlaced(region, "simple20");
region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100));
verifyReadNotPlaced(region, "simple");
verifyReadNotPlaced(region, "overlap_equal");
verifyReadNotPlaced(region, "overlap_unequal");
verifyReadNotPlaced(region, "boundary_equal");
verifyReadNotPlaced(region, "boundary_unequal");
verifyReadNotPlaced(region, "extended_only");
verifyReadNotPlaced(region, "extended_and_np");
verifyReadNotPlaced(region, "outside_intervals");
verifyReadPrimary(region, "simple20");
// TODO: more tests and edge cases
}
@ -282,6 +293,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
for (LocusShardDataProvider dataProvider : createDataProviders(intervals))
t.traverse(walker, dataProvider, 0);
t.endTraversal(walker, 0);
return walker.mappedActiveRegions;
}