From 30ab3af0c88d4d22a6d894c8d5e45863b4957445 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 22 Sep 2011 17:14:59 -0400 Subject: [PATCH] A few more simpleMerge UnitTest tests for filtered vcs --- .../VariantContextUtilsUnitTest.java | 25 ++++++++++++++----- 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index ff26d7245..070fdaca4 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -304,12 +304,6 @@ public class VariantContextUtilsUnitTest extends BaseTest { makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX)); - new MergeFilteredTest("FailOneUnfiltered", - makeVC("1", Arrays.asList(Aref, T), "FAIL"), - makeVC("2", Arrays.asList(Aref, T), "."), - makeVC("3", Arrays.asList(Aref, T), "."), - String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX)); - new MergeFilteredTest("AllFiltered", makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("2", Arrays.asList(Aref, T), "FAIL"), @@ -317,6 +311,13 @@ public class VariantContextUtilsUnitTest extends BaseTest { VariantContextUtils.MERGE_FILTER_IN_ALL); // test ALL vs. ANY + new MergeFilteredTest("FailOneUnfiltered", + makeVC("1", Arrays.asList(Aref, T), "FAIL"), + makeVC("2", Arrays.asList(Aref, T), "."), + makeVC("3", Arrays.asList(Aref, T), "."), + VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX)); + new MergeFilteredTest("OneFailAllUnfilteredArg", makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("2", Arrays.asList(Aref, T), "."), @@ -338,6 +339,18 @@ public class VariantContextUtilsUnitTest extends BaseTest { makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), VariantContextUtils.MERGE_INTERSECTION); + new MergeFilteredTest("RefInAll", + makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), + makeVC("2", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), + makeVC("3", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), + VariantContextUtils.MERGE_REF_IN_ALL); + + new MergeFilteredTest("RefInOne", + makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), + makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), + makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), + "2"); + return MergeFilteredTest.getTests(MergeFilteredTest.class); }