/htsjdk

fixing vararg warnings on test compilation #809

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merged 2 commits into from Mar 7, 2017
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89 src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java
@@ -178,8 +178,8 @@ public void testMultipleSNPAlleleOrdering() {
final List<Allele> allelesUnnaturalOrder = Arrays.asList(Aref, T, C);
VariantContext naturalVC = snpBuilder.alleles(allelesNaturalOrder).make();
VariantContext unnaturalVC = snpBuilder.alleles(allelesUnnaturalOrder).make();
- Assert.assertEquals(new ArrayList<Allele>(naturalVC.getAlleles()), allelesNaturalOrder);
- Assert.assertEquals(new ArrayList<Allele>(unnaturalVC.getAlleles()), allelesUnnaturalOrder);
+ Assert.assertEquals(new ArrayList<>(naturalVC.getAlleles()), allelesNaturalOrder);
+ Assert.assertEquals(new ArrayList<>(unnaturalVC.getAlleles()), allelesUnnaturalOrder);
}
@Test
@@ -371,7 +371,7 @@ public void testBadConstructorArgs3() {
@Test (expectedExceptions = Throwable.class)
public void testBadConstructorArgs4() {
- new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList()).make();
+ new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Collections.emptyList()).make();
}
@Test (expectedExceptions = Exception.class)
@@ -528,7 +528,7 @@ public void testFilters() {
Assert.assertTrue(vc.filtersWereApplied());
Assert.assertNotNull(vc.getFiltersMaybeNull());
- Set<String> filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!", "REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
+ Set<String> filters = new HashSet<>(Arrays.asList("BAD_SNP_BAD!", "REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
vc = new VariantContextBuilder(vc).filters(filters).make();
Assert.assertFalse(vc.isNotFiltered());
@@ -570,12 +570,16 @@ public void testVCFfromGenotypes() {
Genotype g5 = GenotypeBuilder.create("AC", Arrays.asList(Aref, C));
VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g1,g2,g3,g4,g5).make();
- VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g2.getSampleName())), true);
- VariantContext vc1 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName())), true);
- VariantContext vc23 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g2.getSampleName(), g3.getSampleName())), true);
- VariantContext vc4 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g4.getSampleName())), true);
- VariantContext vc14 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g4.getSampleName())), true);
- VariantContext vc125 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g2.getSampleName(), g5.getSampleName())), true);
+ VariantContext vc12 = vc.subContextFromSamples(
+ new HashSet<>(Arrays.asList(g1.getSampleName(), g2.getSampleName())), true);
+ VariantContext vc1 = vc.subContextFromSamples(new HashSet<>(Arrays.asList(g1.getSampleName())), true);
+ VariantContext vc23 = vc.subContextFromSamples(
+ new HashSet<>(Arrays.asList(g2.getSampleName(), g3.getSampleName())), true);
+ VariantContext vc4 = vc.subContextFromSamples(new HashSet<>(Arrays.asList(g4.getSampleName())), true);
+ VariantContext vc14 = vc.subContextFromSamples(
+ new HashSet<>(Arrays.asList(g1.getSampleName(), g4.getSampleName())), true);
+ VariantContext vc125 = vc.subContextFromSamples(
+ new HashSet<>(Arrays.asList(g1.getSampleName(), g2.getSampleName(), g5.getSampleName())), true);
Assert.assertTrue(vc12.isPolymorphicInSamples());
Assert.assertTrue(vc23.isPolymorphicInSamples());
@@ -676,7 +680,7 @@ public String toString() {
@DataProvider(name = "getAlleles")
public Object[][] mergeAllelesData() {
- List<Object[]> tests = new ArrayList<Object[]>();
+ List<Object[]> tests = new ArrayList<>();
tests.add(new Object[]{new GetAllelesTest("A*", Aref)});
tests.add(new Object[]{new GetAllelesTest("A*/C", Aref, C)});
@@ -747,7 +751,7 @@ public String toString() {
VariantContext sites = new VariantContextBuilder("sites", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).make();
VariantContext genotypes = new VariantContextBuilder(sites).source("genotypes").genotypes(g1, g2, g3).make();
- List<Object[]> tests = new ArrayList<Object[]>();
+ List<Object[]> tests = new ArrayList<>();
tests.add(new Object[]{new SitesAndGenotypesVC("sites", sites)});
tests.add(new Object[]{new SitesAndGenotypesVC("genotypes", genotypes)});
@@ -822,7 +826,7 @@ public void runModifyVCTests(SitesAndGenotypesVC cfg) {
boolean updateAlleles;
private SubContextTest(Collection<String> samples, boolean updateAlleles) {
- this.samples = new HashSet<String>(samples);
+ this.samples = new HashSet<>(samples);
this.updateAlleles = updateAlleles;
}
@@ -833,10 +837,10 @@ public String toString() {
@DataProvider(name = "SubContextTest")
public Object[][] MakeSubContextTest() {
- List<Object[]> tests = new ArrayList<Object[]>();
+ List<Object[]> tests = new ArrayList<>();
for ( boolean updateAlleles : Arrays.asList(true, false)) {
- tests.add(new Object[]{new SubContextTest(Collections.<String>emptySet(), updateAlleles)});
+ tests.add(new Object[]{new SubContextTest(Collections.emptySet(), updateAlleles)});
tests.add(new Object[]{new SubContextTest(Collections.singleton("MISSING"), updateAlleles)});
tests.add(new Object[]{new SubContextTest(Collections.singleton("AA"), updateAlleles)});
tests.add(new Object[]{new SubContextTest(Collections.singleton("AT"), updateAlleles)});
@@ -871,7 +875,7 @@ public void runSubContextTest(SubContextTest cfg) {
Assert.assertEquals(sub.getID(), vc.getID());
Assert.assertEquals(sub.getAttributes(), vc.getAttributes());
- Set<Genotype> expectedGenotypes = new HashSet<Genotype>();
+ Set<Genotype> expectedGenotypes = new HashSet<>();
if ( cfg.samples.contains(g1.getSampleName()) ) expectedGenotypes.add(g1);
if ( cfg.samples.contains(g2.getSampleName()) ) expectedGenotypes.add(g2);
if ( cfg.samples.contains(g3.getSampleName()) ) expectedGenotypes.add(g3);
@@ -881,10 +885,10 @@ public void runSubContextTest(SubContextTest cfg) {
// these values depend on the results of sub
if ( cfg.updateAlleles ) {
// do the work to see what alleles should be here, and which not
- List<Allele> expectedAlleles = new ArrayList<Allele>();
+ List<Allele> expectedAlleles = new ArrayList<>();
expectedAlleles.add(Aref);
- Set<Allele> genotypeAlleles = new HashSet<Allele>();
+ Set<Allele> genotypeAlleles = new HashSet<>();
for ( final Genotype g : expectedGC )
genotypeAlleles.addAll(g.getAlleles());
genotypeAlleles.remove(Aref);
@@ -925,7 +929,7 @@ public String toString() {
@DataProvider(name = "SampleNamesTest")
public Object[][] MakeSampleNamesTest() {
- List<Object[]> tests = new ArrayList<Object[]>();
+ List<Object[]> tests = new ArrayList<>();
tests.add(new Object[]{new SampleNamesTest(Arrays.asList("1"), Arrays.asList("1"))});
tests.add(new Object[]{new SampleNamesTest(Arrays.asList("2", "1"), Arrays.asList("1", "2"))});
@@ -959,7 +963,7 @@ public void runSampleNamesTest(SampleNamesTest cfg) {
VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).genotypes(gc).make();
// same sample names => success
- Assert.assertTrue(vc.getSampleNames().equals(new HashSet<String>(cfg.sampleNames)), "vc.getSampleNames() = " + vc.getSampleNames());
+ Assert.assertTrue(vc.getSampleNames().equals(new HashSet<>(cfg.sampleNames)), "vc.getSampleNames() = " + vc.getSampleNames());
Assert.assertEquals(vc.getSampleNamesOrderedByName(), cfg.sampleNamesInOrder, "vc.getSampleNamesOrderedByName() = " + vc.getSampleNamesOrderedByName());
assertGenotypesAreInOrder(vc.getGenotypesOrderedByName(), cfg.sampleNamesInOrder);
@@ -1147,7 +1151,7 @@ private VariantContext createTestVariantContextRsIds(final String rsId) {
fullyDecoded, toValidate);
}
private Set<String> makeRsIDsSet(final String... rsIds) {
- return new HashSet<String>(Arrays.asList(rsIds));
+ return new HashSet<>(Arrays.asList(rsIds));
}
@@ -1226,64 +1230,65 @@ private VariantContext createValidateAlternateAllelesContext(final List<Allele>
/** AN : total number of alleles in called genotypes **/
// with AN set and hom-ref, we expect AN to be 2 for Aref/Aref
- final Map<String, Object> attributesAN = new HashMap<String, Object>();
+ final Map<String, Object> attributesAN = new HashMap<>();
attributesAN.put(VCFConstants.ALLELE_NUMBER_KEY, "2");
final VariantContext vcANSet =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesAN, homRef);
// with AN set, one no-call (no-calls get ignored by getCalledChrCount() in VariantContext)
// we expect AN to be 1 for Aref/no-call
- final Map<String, Object> attributesANNoCall = new HashMap<String, Object>();
+ final Map<String, Object> attributesANNoCall = new HashMap<>();
attributesANNoCall.put(VCFConstants.ALLELE_NUMBER_KEY, "1");
final VariantContext vcANSetNoCall =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesANNoCall, homRefNoCall);
/** AC : allele count in genotypes, for each ALT allele, in the same order as listed **/
// with AC set, and T/T, we expect AC to be 2 (for 2 counts of ALT T)
- final Map<String, Object> attributesAC = new HashMap<String, Object>();
+ final Map<String, Object> attributesAC = new HashMap<>();
attributesAC.put(VCFConstants.ALLELE_COUNT_KEY, "2");
final VariantContext vcACSet =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T), attributesAC, homVarT);
// with AC set and no ALT (GT is 0/0), we expect AC count to be 0
- final Map<String, Object> attributesACNoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesACNoAlts = new HashMap<>();
attributesACNoAlts.put(VCFConstants.ALLELE_COUNT_KEY, "0");
final VariantContext vcACSetNoAlts =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesACNoAlts, homRef);
// with AC set, and two different ALTs (T and C), with GT of 1/2, we expect a count of 1 for each.
// With two ALTs, a list is expected, so we set the attribute as a list of 1,1
- final Map<String, Object> attributesACTwoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesACTwoAlts = new HashMap<>();
attributesACTwoAlts.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1", "1"));
final VariantContext vcACSetTwoAlts =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAlts, hetVarTC);
// with AC set, and two different ALTs (T and C), with no GT, we expect a 2 count values.
- final Map<String, Object> attributesACNoGtTwoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesACNoGtTwoAlts = new HashMap<>();
attributesACNoGtTwoAlts.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1", "1"));
final VariantContext vcACNoGtSetTwoAlts =
- createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAlts, null);
+ createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAlts, (Genotype[]) null);
// with AF set, and two different ALTs (T and C), with GT of 1/2, we expect two frequncy values.
// With two ALTs, a list is expected, so we set the attribute as a list of 0.5,0.5
- final Map<String, Object> attributesAFTwoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesAFTwoAlts = new HashMap<>();
attributesAFTwoAlts.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5", "0.5"));
final VariantContext vcAFSetTwoAlts =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFTwoAlts, hetVarTC);
// with AF set, and two different ALTs (T and C), with no GT, we expect two frequency values.
- final Map<String, Object> attributesAFNoGtTwoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesAFNoGtTwoAlts = new HashMap<>();
attributesAFNoGtTwoAlts.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5", "0.5"));
final VariantContext vcAFNoGtSetTwoAlts =
- createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAlts, null);
+ createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAlts, (Genotype[]) null);
return new Object[][]{
{vcNoGenotypes},
{vcANSet},
{vcANSetNoCall},
{vcACSet},
{vcACSetNoAlts},
+ {vcACSetTwoAlts},
{vcACNoGtSetTwoAlts},
{vcAFSetTwoAlts},
{vcAFNoGtSetTwoAlts}
@@ -1303,60 +1308,60 @@ public void testValidateChromosomeCounts(final VariantContext vc) {
/** AN : total number of alleles in called genotypes **/
// with AN set and hom-ref, we expect AN to be 2 for Aref/Aref, so 3 will fail
- final Map<String, Object> attributesAN = new HashMap<String, Object>();
+ final Map<String, Object> attributesAN = new HashMap<>();
attributesAN.put(VCFConstants.ALLELE_NUMBER_KEY, "3");
final VariantContext vcANSet =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesAN, homRef);
// with AN set, one no-call (no-calls get ignored by getCalledChrCount() in VariantContext)
// we expect AN to be 1 for Aref/no-call, so 2 will fail
- final Map<String, Object> attributesANNoCall = new HashMap<String, Object>();
+ final Map<String, Object> attributesANNoCall = new HashMap<>();
attributesANNoCall.put(VCFConstants.ALLELE_NUMBER_KEY, "2");
final VariantContext vcANSetNoCall =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesANNoCall, homRefNoCall);
/** AC : allele count in genotypes, for each ALT allele, in the same order as listed **/
// with AC set but no ALTs, we expect a count of 0, so the wrong count will fail here
- final Map<String, Object> attributesACWrongCount = new HashMap<String, Object>();
+ final Map<String, Object> attributesACWrongCount = new HashMap<>();
attributesACWrongCount.put(VCFConstants.ALLELE_COUNT_KEY, "2");
final VariantContext vcACWrongCount =
createValidateChromosomeCountsContext(Arrays.asList(Aref), attributesACWrongCount, homRef);
// with AC set, two ALTs, but AC is not a list with count for each ALT
- final Map<String, Object> attributesACTwoAlts = new HashMap<String, Object>();
+ final Map<String, Object> attributesACTwoAlts = new HashMap<>();
attributesACTwoAlts.put(VCFConstants.ALLELE_COUNT_KEY, "1");
final VariantContext vcACSetTwoAlts =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAlts, hetVarTC);
// with AC set, two ALTs, and a list is correctly used, but wrong counts (we expect counts to be 1,1)
- final Map<String, Object> attributesACTwoAltsWrongCount = new HashMap<String, Object>();
+ final Map<String, Object> attributesACTwoAltsWrongCount = new HashMap<>();
attributesACTwoAltsWrongCount.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1", "2"));
final VariantContext vcACSetTwoAltsWrongCount =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAltsWrongCount, hetVarTC);
// with AC set, two ALTs, but only count for one ALT (we expect two items in the list: 1,1)
- final Map<String, Object> attributesACTwoAltsOneAltCount = new HashMap<String, Object>();
+ final Map<String, Object> attributesACTwoAltsOneAltCount = new HashMap<>();
attributesACTwoAltsOneAltCount.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1"));
final VariantContext vcACSetTwoAltsOneAltCount =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACTwoAltsOneAltCount, hetVarTC);
// with AC set, no GT, two ALTs, but only count for one ALT (we expect two items in the list: 1,1)
- final Map<String, Object> attributesACNoGtTwoAltsOneAltCount = new HashMap<String, Object>();
+ final Map<String, Object> attributesACNoGtTwoAltsOneAltCount = new HashMap<>();
attributesACNoGtTwoAltsOneAltCount.put(VCFConstants.ALLELE_COUNT_KEY, Arrays.asList("1"));
final VariantContext vcACNoGtSetTwoAltsOneAltCount =
- createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAltsOneAltCount, null);
+ createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesACNoGtTwoAltsOneAltCount, (Genotype[])null);
// with AF set, two ALTs, but only frequency for one ALT (we expect two items in the list
- final Map<String, Object> attributesAFTwoAltsWrongFreq = new HashMap<String, Object>();
+ final Map<String, Object> attributesAFTwoAltsWrongFreq = new HashMap<>();
attributesAFTwoAltsWrongFreq.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5"));
final VariantContext vcAFSetTwoAltsWrongFreq =
createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFTwoAltsWrongFreq, hetVarTC);
// with AF set, no GT, two ALTs, but only frequency for one ALT (we expect two items in the list
- final Map<String, Object> attributesAFNoGtTwoAltsWrongCount = new HashMap<String, Object>();
+ final Map<String, Object> attributesAFNoGtTwoAltsWrongCount = new HashMap<>();
attributesAFNoGtTwoAltsWrongCount.put(VCFConstants.ALLELE_FREQUENCY_KEY, Arrays.asList("0.5"));
final VariantContext vcAFNoGtSetTwoAltsWrongFreq =
- createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAltsWrongCount, null);
+ createValidateChromosomeCountsContext(Arrays.asList(Aref, T, C), attributesAFNoGtTwoAltsWrongCount, (Genotype[])null);
return new Object[][]{
{vcANSet},