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 a65b0cb45..b08210ea6 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -109,6 +109,8 @@ public class TraverseActiveRegionsTest extends BaseTest { dictionary = reference.getSequenceDictionary(); genomeLocParser = new GenomeLocParser(dictionary); + // TODO: test shard boundaries + intervals = new ArrayList(); intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20)); intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999)); @@ -139,8 +141,6 @@ public class TraverseActiveRegionsTest extends BaseTest { List activeIntervals = getIsActiveIntervals(walker, intervals); // Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call verifyEqualIntervals(intervals, activeIntervals); - - // TODO: more tests and edge cases } private List getIsActiveIntervals(DummyActiveRegionWalker walker, List intervals) { @@ -171,8 +171,6 @@ public class TraverseActiveRegionsTest extends BaseTest { Collection activeRegions = getActiveRegions(walker, intervals).values(); verifyActiveRegionCoverage(intervals, activeRegions); - - // TODO: more tests and edge cases } private void verifyActiveRegionCoverage(List intervals, Collection activeRegions) { @@ -279,8 +277,6 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); getRead(region, "simple20"); - - // TODO: more tests and edge cases } @Test @@ -348,8 +344,6 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); getRead(region, "simple20"); - - // TODO: more tests and edge cases } @Test @@ -418,8 +412,11 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); getRead(region, "simple20"); + } - // TODO: more tests and edge cases + @Test + public void testUnmappedReads() { + // TODO } private void verifyReadNotPlaced(ActiveRegion region, String readName) {