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A few more simpleMerge UnitTest tests for filtered vcs

This commit is contained in:
Mark DePristo 2011-09-22 17:14:59 -04:00
parent 5cf82f9236
commit 30ab3af0c8
1 changed files with 19 additions and 6 deletions
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25
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
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@ -304,12 +304,6 @@ public class VariantContextUtilsUnitTest extends BaseTest {
makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX)); 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", new MergeFilteredTest("AllFiltered",
makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("1", Arrays.asList(Aref, T), "FAIL"),
makeVC("2", 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); VariantContextUtils.MERGE_FILTER_IN_ALL);
// test ALL vs. ANY // 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", new MergeFilteredTest("OneFailAllUnfilteredArg",
makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("1", Arrays.asList(Aref, T), "FAIL"),
makeVC("2", Arrays.asList(Aref, T), "."), makeVC("2", Arrays.asList(Aref, T), "."),
@ -338,6 +339,18 @@ public class VariantContextUtilsUnitTest extends BaseTest {
makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
VariantContextUtils.MERGE_INTERSECTION); 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); return MergeFilteredTest.getTests(MergeFilteredTest.class);
} }