private static void addGenotypesAndGTests() {
// for ( final int ploidy : Arrays.asList(2)) {
for (final int ploidy : Arrays.asList(1, 2, 3, 4, 5)) {
final List<List<String>> alleleCombinations =
Arrays.asList(
Arrays.asList("A"),
Arrays.asList("A", "C"),
Arrays.asList("A", "C", "G"),
Arrays.asList("A", "C", "G", "T"));
for (final List<String> alleles : alleleCombinations) {
final VariantContextBuilder vcb = builder().alleles(alleles);
final VariantContext site = vcb.make();
final int nAlleles = site.getNAlleles();
final Allele ref = site.getReference();
// base genotype is ref/.../ref up to ploidy
final List<Allele> baseGenotype = new ArrayList<Allele>(ploidy);
for (int i = 0; i < ploidy; i++) baseGenotype.add(ref);
final int nPLs = GenotypeLikelihoods.numLikelihoods(nAlleles, ploidy);
// ada is 0, 1, ..., nAlleles - 1
final List<Integer> ada = new ArrayList<Integer>(nAlleles);
for (int i = 0; i < nAlleles - 1; i++) ada.add(i);
// pl is 0, 1, ..., up to nPLs (complex calc of nAlleles and ploidy)
final int[] pl = new int[nPLs];
for (int i = 0; i < pl.length; i++) pl[i] = i;
final GenotypeBuilder gb = new GenotypeBuilder("ADA_PL_SAMPLE");
gb.alleles(baseGenotype);
gb.PL(pl);
gb.attribute("ADA", nAlleles == 2 ? ada.get(0) : ada);
vcb.genotypes(gb.make());
add(vcb);
}
}
}
private static void addGenotypes(final VariantContext site) {
// test ref/ref
final Allele ref = site.getReference();
final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null;
final Genotype homRef = GenotypeBuilder.create("homRef", Arrays.asList(ref, ref));
addGenotypeTests(site, homRef);
if (alt1 != null) {
final Genotype het = GenotypeBuilder.create("het", Arrays.asList(ref, alt1));
final Genotype homVar = GenotypeBuilder.create("homVar", Arrays.asList(alt1, alt1));
addGenotypeTests(site, homRef, het);
addGenotypeTests(site, homRef, het, homVar);
// test no GT at all
addGenotypeTests(
site, new GenotypeBuilder("noGT", new ArrayList<Allele>(0)).attribute("INT1", 10).make());
final List<Allele> noCall = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
// ploidy
if (ENABLE_PLOIDY_TESTS) {
addGenotypeTests(
site,
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("hap", Arrays.asList(ref)));
addGenotypeTests(
site,
GenotypeBuilder.create("noCall", noCall),
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("hap", Arrays.asList(ref)));
addGenotypeTests(
site,
GenotypeBuilder.create("noCall", noCall),
GenotypeBuilder.create("noCall2", noCall),
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("hap", Arrays.asList(ref)));
addGenotypeTests(
site,
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1)));
addGenotypeTests(
site,
GenotypeBuilder.create("noCall", noCall),
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1)));
addGenotypeTests(
site,
GenotypeBuilder.create("noCall", noCall),
GenotypeBuilder.create("noCall2", noCall),
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1)));
addGenotypeTests(
site,
GenotypeBuilder.create("nocall", noCall),
GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)),
GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1)));
}
//
//
// TESTING PHASE
//
//
final Genotype gUnphased = new GenotypeBuilder("gUnphased", Arrays.asList(ref, alt1)).make();
final Genotype gPhased =
new GenotypeBuilder("gPhased", Arrays.asList(ref, alt1)).phased(true).make();
final Genotype gPhased2 =
new GenotypeBuilder("gPhased2", Arrays.asList(alt1, alt1)).phased(true).make();
final Genotype gPhased3 =
new GenotypeBuilder("gPhased3", Arrays.asList(ref, ref)).phased(true).make();
final Genotype haploidNoPhase =
new GenotypeBuilder("haploidNoPhase", Arrays.asList(ref)).make();
addGenotypeTests(site, gUnphased, gPhased);
addGenotypeTests(site, gUnphased, gPhased2);
addGenotypeTests(site, gUnphased, gPhased3);
addGenotypeTests(site, gPhased, gPhased2);
addGenotypeTests(site, gPhased, gPhased3);
addGenotypeTests(site, gPhased2, gPhased3);
addGenotypeTests(site, haploidNoPhase, gPhased);
addGenotypeTests(site, haploidNoPhase, gPhased2);
addGenotypeTests(site, haploidNoPhase, gPhased3);
addGenotypeTests(site, haploidNoPhase, gPhased, gPhased2);
addGenotypeTests(site, haploidNoPhase, gPhased, gPhased3);
addGenotypeTests(site, haploidNoPhase, gPhased2, gPhased3);
addGenotypeTests(site, haploidNoPhase, gPhased, gPhased2, gPhased3);
final Genotype gUnphasedTet =
new GenotypeBuilder("gUnphasedTet", Arrays.asList(ref, alt1, ref, alt1)).make();
final Genotype gPhasedTet =
new GenotypeBuilder("gPhasedTet", Arrays.asList(ref, alt1, alt1, alt1))
.phased(true)
.make();
addGenotypeTests(site, gUnphasedTet, gPhasedTet);
}
if (ENABLE_PL_TESTS) {
if (site.getNAlleles() == 2) {
// testing PLs
addGenotypeTests(
site,
GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {0, -1, -2}),
GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2, -3}));
addGenotypeTests(
site,
GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}),
GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2, -3}));
addGenotypeTests(
site,
GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}),
GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2000, -1000}));
addGenotypeTests(
site, // missing PLs
GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}),
GenotypeBuilder.create("g2", Arrays.asList(ref, ref)));
} else if (site.getNAlleles() == 3) {
// testing PLs
addGenotypeTests(
site,
GenotypeBuilder.create(
"g1", Arrays.asList(ref, ref), new double[] {0, -1, -2, -3, -4, -5}),
GenotypeBuilder.create(
"g2", Arrays.asList(ref, ref), new double[] {0, -2, -3, -4, -5, -6}));
}
}
// test attributes
addGenotypeTests(site, attr("g1", ref, "INT1", 1), attr("g2", ref, "INT1", 2));
addGenotypeTests(site, attr("g1", ref, "INT1", 1), attr("g2", ref, "INT1"));
addGenotypeTests(site, attr("g1", ref, "INT3", 1, 2, 3), attr("g2", ref, "INT3", 4, 5, 6));
addGenotypeTests(site, attr("g1", ref, "INT3", 1, 2, 3), attr("g2", ref, "INT3"));
addGenotypeTests(
site, attr("g1", ref, "INT20", TWENTY_INTS), attr("g2", ref, "INT20", TWENTY_INTS));
if (ENABLE_VARARRAY_TESTS) {
addGenotypeTests(
site,
attr("g1", ref, "INT.VAR", 1, 2, 3),
attr("g2", ref, "INT.VAR", 4, 5),
attr("g3", ref, "INT.VAR", 6));
addGenotypeTests(
site,
attr("g1", ref, "INT.VAR", 1, 2, 3),
attr("g2", ref, "INT.VAR"),
attr("g3", ref, "INT.VAR", 5));
}
addGenotypeTests(site, attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "FLOAT1", 2.0));
addGenotypeTests(site, attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "FLOAT1"));
addGenotypeTests(
site, attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0), attr("g2", ref, "FLOAT3", 4.0, 5.0, 6.0));
addGenotypeTests(site, attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0), attr("g2", ref, "FLOAT3"));
if (ENABLE_VARIABLE_LENGTH_GENOTYPE_STRING_TESTS) {
//
//
// TESTING MULTIPLE SIZED LISTS IN THE GENOTYPE FIELD
//
//
addGenotypeTests(
site,
attr("g1", ref, "GS", Arrays.asList("S1", "S2")),
attr("g2", ref, "GS", Arrays.asList("S3", "S4")));
addGenotypeTests(
site, // g1 is missing the string, and g2 is missing FLOAT1
attr("g1", ref, "FLOAT1", 1.0),
attr("g2", ref, "GS", Arrays.asList("S3", "S4")));
// variable sized lists
addGenotypeTests(
site, attr("g1", ref, "GV", "S1"), attr("g2", ref, "GV", Arrays.asList("S3", "S4")));
addGenotypeTests(
site,
attr("g1", ref, "GV", Arrays.asList("S1", "S2")),
attr("g2", ref, "GV", Arrays.asList("S3", "S4", "S5")));
addGenotypeTests(
site, // missing value in varlist of string
attr("g1", ref, "FLOAT1", 1.0),
attr("g2", ref, "GV", Arrays.asList("S3", "S4", "S5")));
}
//
//
// TESTING GENOTYPE FILTERS
//
//
addGenotypeTests(
site,
new GenotypeBuilder("g1-x", Arrays.asList(ref, ref)).filters("X").make(),
new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make());
addGenotypeTests(
site,
new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(),
new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make());
addGenotypeTests(
site,
new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(),
new GenotypeBuilder("g2-xy", Arrays.asList(ref, ref)).filters("X", "Y").make());
addGenotypeTests(
site,
new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(),
new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make(),
new GenotypeBuilder("g3-xy", Arrays.asList(ref, ref)).filters("X", "Y").make());
}
