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Add additional LiftoverVcf tests #1011

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Dec 15, 2017
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Add additional LiftoverVcf tests #1011

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157 changes: 118 additions & 39 deletions src/test/java/picard/util/LiftoverVcfTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@ public class LiftoverVcfTest extends CommandLineProgramTest {

private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("LiftoverVcfsTest", null);

private final int CHAIN_SIZE = 540; // the length of the single chain in CHAIN_FILE

public String getCommandLineProgramName() {
return LiftoverVcf.class.getSimpleName();
}
Expand All @@ -51,7 +53,7 @@ public void teardown() {
@DataProvider(name = "liftoverReverseStrand")
public Object[][] liftoverReverseStrand() {
return new Object[][]{
{"testLiftoverBiallelicIndels.vcf", 3, 0},
{"testLiftoverBiallelicIndels.vcf", 5, 0},
{"testLiftoverMultiallelicIndels.vcf", 0, 2},
{"testLiftoverFailingVariants.vcf", 3, 0},
};
Expand Down Expand Up @@ -195,6 +197,9 @@ public void testWriteOriginalPosition(final boolean shouldWriteOriginalPosition)
}
}

private static final ReferenceSequence REFERENCE = new ReferenceSequence("chr1", 0, "CAAAAAAAAAACGTACGTACTCTCTCTCTACGT".getBytes());
// 123456789 123456789 123456789 123

@Test
public void testWriteVcfWithFlippedAlleles() {
final File liftOutputFile = new File(OUTPUT_DATA_PATH, "lift-delete-me.vcf");
Expand Down Expand Up @@ -228,10 +233,6 @@ public void testWriteVcfWithFlippedAlleles() {
@DataProvider(name = "indelFlipData")
public Iterator<Object[]> indelFlipData() {

final ReferenceSequence reference = new ReferenceSequence("chr1", 0,
"CAAAAAAAAAACGTACGTACTCTCTCTCTACGT".getBytes());
// 123456789 123456789 123456789 123

final Allele RefCAA = Allele.create("CAA", true);
final Allele RefGTT = Allele.create("GTT", true);
final Allele RefACGT = Allele.create("ACGT", true);
Expand Down Expand Up @@ -261,8 +262,6 @@ public Iterator<Object[]> indelFlipData() {

final List<Object[]> tests = new ArrayList<>();

final int CHAIN_SIZE = 540; // the length of the single chain in CHAIN_FILE

final VariantContextBuilder builder = new VariantContextBuilder().source("test1").chr("chr1");
final GenotypeBuilder genotypeBuilder = new GenotypeBuilder("test1");
final GenotypeBuilder resultGenotypeBuilder = new GenotypeBuilder("test1");
Expand All @@ -280,7 +279,7 @@ public Iterator<Object[]> indelFlipData() {
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

//simple insertion
// T*/TTT -> A*/AAA -> turns into left-aligned C*/CAA at position 1
Expand All @@ -292,7 +291,7 @@ public Iterator<Object[]> indelFlipData() {
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

builder.noGenotypes();
result_builder.noGenotypes();
Expand All @@ -309,7 +308,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// "CAAAAAAAAAACG---CGTACTCTCTCTCTACGT" -- Allele A
// "CAAAAAAAAAACGacgCGTACTCTCTCTCTACGT" -- Allele B
Expand All @@ -332,7 +331,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// just outside of chain & contig, testing that we do not read into negative indices
// or reference
Expand All @@ -343,7 +342,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// outside of chain
start = stop = CHAIN_SIZE + 1;
Expand All @@ -352,7 +351,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, null});
tests.add(new Object[]{builder.make(), REFERENCE, null});

// MNP
// GTT*(T)/ACGT(T) -> AAA(C)*/AACG(T) -> which is then normalized to A*/CG at position 11
Expand All @@ -365,7 +364,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// MNP
// ACGT*(T)/ATT*(T) -> AACG(T)*/AAA(T) -> by normalization CG(T)*/A(T)
Expand All @@ -378,7 +377,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// needs left-aligning
// T->TAG --> T(A)/TCT(A) -> by normalization A/ACT @ 19
Expand All @@ -391,7 +390,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// insertion at end of section
// a test that converts the initial C to a AC which requires
Expand All @@ -408,7 +407,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// insertion at end of section
// a test that converts the initial C to a AC which requires
Expand All @@ -425,7 +424,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// insertion at end of section
// a test that converts the initial C to a AC which requires
Expand All @@ -442,7 +441,7 @@ public Iterator<Object[]> indelFlipData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

return tests.iterator();
}
Expand Down Expand Up @@ -530,10 +529,6 @@ public void snpWithChangedRef(final VariantContext source, final ReferenceSequen
@DataProvider(name = "leftAlignAllelesData")
public Iterator<Object[]> leftAlignAllelesData() {

final ReferenceSequence reference = new ReferenceSequence("chr1", 0,
"CAAAAAAAAAACGTACGTACTCTCTCTCTACGT".getBytes());
// 123456789 123456789 123456789 123

final Allele RefG = Allele.create("G", true);
final Allele A = Allele.create("A", false);

Expand Down Expand Up @@ -579,7 +574,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

// simple SNP
// G*/A -> G/A
Expand All @@ -592,20 +587,20 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

for (start = 1; start <= reference.getBases().length; start++) {
for (start = 1; start <= REFERENCE.getBases().length; start++) {
builder.source("test2-" + start);
builder.start(start).stop(start);
builder.alleles(CollectionUtil.makeList(
Allele.create(reference.getBaseString().substring(start - 1, start), true),
reference.getBaseString().charAt(start - 1) == 'A' ? T : A));
Allele.create(REFERENCE.getBaseString().substring(start - 1, start), true),
REFERENCE.getBaseString().charAt(start - 1) == 'A' ? T : A));

genotypeBuilder.alleles(builder.getAlleles());
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, builder.make()});
}

// AA/A in initial polyA repeat -> CA/C at the beginning
Expand All @@ -620,7 +615,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

// A/AA in initial polyA repeat -> C/CA at the beginning
Expand All @@ -635,7 +630,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

//CT/CTCT -> A/ACT in CT repeat region
Expand All @@ -650,7 +645,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

//TC/TCTC -> A/ACT in CT repeat region
Expand All @@ -664,7 +659,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

//CTCT/CT -> ACT/A in CT repeat region
Expand All @@ -679,7 +674,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

//TCTC/TC-> ACT/A in CT repeat region
Expand All @@ -693,7 +688,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}

// for ease of reading, here's the reference sequence
Expand All @@ -706,13 +701,13 @@ public Iterator<Object[]> leftAlignAllelesData() {
builder.source("test9-" + start + "-" + stop);
builder.alleles(
// -1 here due to reference string being 0-based.
reference.getBaseString().substring(start - 1, stop + 1 - 1),
reference.getBaseString().substring(start - 1, stop - 3 - 1)).start(start).stop(stop);
REFERENCE.getBaseString().substring(start - 1, stop + 1 - 1),
REFERENCE.getBaseString().substring(start - 1, stop - 3 - 1)).start(start).stop(stop);
genotypeBuilder.alleles(builder.getAlleles());
resultGenotypeBuilder.alleles(result_builder.getAlleles());
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});
}
}

Expand Down Expand Up @@ -743,7 +738,7 @@ public Iterator<Object[]> leftAlignAllelesData() {
result_builder.genotypes(results_genotypes);

builder.source("test12");
tests.add(new Object[]{builder.make(), reference, result_builder.make()});
tests.add(new Object[]{builder.make(), REFERENCE, result_builder.make()});

return tests.iterator();
}
Expand Down Expand Up @@ -952,4 +947,88 @@ public void testLiftOverSimpleIndels(final LiftOver liftOver, final ReferenceSeq
VcfTestUtils.assertEquals(vcb == null ? null : vcb.make(), result);
}

@DataProvider(name = "noCallAndSymbolicData")
public Iterator<Object[]> noCallAndSymbolicData() {

final VariantContextBuilder builder = new VariantContextBuilder().source("test1").chr("chr1");
final VariantContextBuilder result_builder = new VariantContextBuilder().source("test1").chr("chr1");
final GenotypeBuilder genotypeBuilder = new GenotypeBuilder("test1");
final GenotypeBuilder resultGenotypeBuilder = new GenotypeBuilder("test1");
final List<Object[]> tests = new ArrayList<>();

final Allele CRef = Allele.create("C", true);
final Allele GRef = Allele.create("G", true);
final Allele T = Allele.create("T", false);
final Allele A = Allele.create("A", false);
final Allele DEL = Allele.create("*", false);

final LiftOver liftOver = new LiftOver(TWO_INTERVAL_CHAIN_FILE);
final LiftOver liftOverRC = new LiftOver(CHAIN_FILE);

builder.source("test1");
int start = 10;
builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T));
result_builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T));
genotypeBuilder.alleles(CollectionUtil.makeList(Allele.create("."), Allele.create(".")));
resultGenotypeBuilder.alleles(CollectionUtil.makeList(Allele.create("."), Allele.create(".")));
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{liftOver, builder.make(), result_builder.make(), false});

builder.source("test2");
builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T, DEL));
result_builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T, DEL));
genotypeBuilder.alleles(CollectionUtil.makeList(T, DEL));
resultGenotypeBuilder.alleles(CollectionUtil.makeList(T, DEL));
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{liftOver, builder.make(), result_builder.make(), false});

//reverse complement
builder.source("test3");
int offset = 3;
start = CHAIN_SIZE - offset;
int liftedStart = 1 + offset;
builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T, DEL));
result_builder.start(liftedStart).stop(liftedStart).alleles(CollectionUtil.makeList(GRef, A, DEL));

genotypeBuilder.alleles(CollectionUtil.makeList(T, DEL));
resultGenotypeBuilder.alleles(CollectionUtil.makeList(A, DEL));
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{liftOverRC, builder.make(), result_builder.make(), true});

builder.source("test4");
offset = 4;
start = CHAIN_SIZE - offset;
liftedStart = 1 + offset;
builder.start(start).stop(start).alleles(CollectionUtil.makeList(CRef, T));
result_builder.start(liftedStart).stop(liftedStart).alleles(CollectionUtil.makeList(GRef, A));

genotypeBuilder.alleles(CollectionUtil.makeList(T, Allele.NO_CALL));
resultGenotypeBuilder.alleles(CollectionUtil.makeList(A, Allele.NO_CALL));
builder.genotypes(genotypeBuilder.make());
result_builder.genotypes(resultGenotypeBuilder.make());

tests.add(new Object[]{liftOverRC, builder.make(), result_builder.make(), true});

return tests.iterator();
}

@Test(dataProvider = "noCallAndSymbolicData")
public void testLiftOverNoCallAndSymbolic(final LiftOver liftOver, final VariantContext source, final VariantContext result, final boolean expectReversed) {

final Interval target = liftOver.liftOver(new Interval(source.getContig(), source.getStart(), source.getEnd()), .95);

Assert.assertEquals(target.isNegativeStrand(), expectReversed);

VariantContext vc = LiftoverUtils.liftVariant(source, target, REFERENCE, true);
VcfTestUtils.assertEquals(vc, result);

Assert.assertEquals(vc.getAttribute(LiftoverVcf.ORIGINAL_CONTIG), source.getContig());
Assert.assertEquals(vc.getAttribute(LiftoverVcf.ORIGINAL_START), source.getStart());
}
}
4 changes: 3 additions & 1 deletion testdata/picard/vcf/testLiftoverBiallelicIndels.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,6 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
chr1 1 . C CCCCT 15676.17 PASS . GT 0/0
chr1 61 . GT G 724.43 PASS . GT 0/1
chr1 72 . T A 100 PASS . GT 0/1
chr1 72 . T A 100 PASS . GT 0/1
chr1 72 . T A 100 PASS . GT ./.
chr1 72 . TT A 100 PASS . GT 1/.