From cc550b4145bd8f439a46e407ba015eaeea36edea Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 26 Nov 2012 11:48:05 -0500 Subject: [PATCH] Add a read and interval on a different contig --- .../traversals/TraverseActiveRegionsTest.java | 27 ++++++++++++++----- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java index e4c7b2db0..018e92d84 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -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(); @@ -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 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; }