@Test(dataProvider = "mergeFiltered")
public void testMergeFiltered(MergeFilteredTest cfg) {
final List<String> priority = vcs2priority(cfg.inputs);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
cfg.inputs,
priority,
cfg.type,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
true,
false,
"set",
false,
false);
// test alleles are equal
Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
// test set field
Assert.assertEquals(merged.getAttribute("set"), cfg.setExpected);
// test filter field
Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
}
@Test
public void testAnnotationSet() {
for (final boolean annotate : Arrays.asList(true, false)) {
for (final String set : Arrays.asList("set", "combine", "x")) {
final List<String> priority = Arrays.asList("1", "2");
VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
Arrays.asList(vc1, vc2),
priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
annotate,
false,
set,
false,
false);
if (annotate)
Assert.assertEquals(merged.getAttribute(set), VariantContextUtils.MERGE_INTERSECTION);
else Assert.assertFalse(merged.hasAttribute(set));
}
}
}
@Test(dataProvider = "mergeAlleles")
public void testMergeAlleles(MergeAllelesTest cfg) {
final List<VariantContext> inputs = new ArrayList<VariantContext>();
int i = 0;
for (final List<Allele> alleles : cfg.inputs) {
final String name = "vcf" + ++i;
inputs.add(makeVC(name, alleles));
}
final List<String> priority = vcs2priority(inputs);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
inputs,
priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
false,
false,
"set",
false,
false);
Assert.assertEquals(merged.getAlleles(), cfg.expected);
}
@Test(expectedExceptions = UserException.class)
public void testMergeGenotypesRequireUnique() {
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
Arrays.asList(vc1, vc2),
null,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE,
false,
false,
"set",
false,
false);
}
@Test(dataProvider = "mergeGenotypes")
public void testMergeGenotypes(MergeGenotypesTest cfg) {
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
cfg.inputs,
cfg.priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
true,
false,
"set",
false,
false);
// test alleles are equal
Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
// test genotypes
assertGenotypesAreMostlyEqual(merged.getGenotypes(), cfg.expected.getGenotypes());
}
@Test
public void testMergeGenotypesUniquify() {
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
Arrays.asList(vc1, vc2),
null,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.UNIQUIFY,
false,
false,
"set",
false,
false);
// test genotypes
Assert.assertEquals(
merged.getSampleNames(), new HashSet<String>(Arrays.asList("s1.1", "s1.2")));
}
@Test(dataProvider = "simplemergersiddata")
public void testRSIDMerge(SimpleMergeRSIDTest cfg) {
VariantContext snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T));
final List<VariantContext> inputs = new ArrayList<VariantContext>();
for (final String id : cfg.inputs) {
inputs.add(new VariantContextBuilder(snpVC1).id(id).make());
}
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
inputs,
null,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.UNSORTED,
false,
false,
"set",
false,
false);
Assert.assertEquals(merged.getID(), cfg.expected);
}
