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include recovered SVS in copy number segments
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94 changes: 94 additions & 0 deletions
94
...oidy-estimator/src/main/java/com/hartwig/hmftools/purple/sv/VariantContextCollection.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| package com.hartwig.hmftools.purple.sv; | ||
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| import java.util.Iterator; | ||
| import java.util.List; | ||
| import java.util.TreeSet; | ||
| import java.util.function.Predicate; | ||
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| import com.google.common.collect.Lists; | ||
| import com.hartwig.hmftools.common.variant.structural.StructuralVariant; | ||
| import com.hartwig.hmftools.common.variant.structural.StructuralVariantFactory; | ||
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| import org.jetbrains.annotations.NotNull; | ||
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| import htsjdk.samtools.SAMSequenceDictionary; | ||
| import htsjdk.variant.variantcontext.VariantContext; | ||
| import htsjdk.variant.variantcontext.VariantContextComparator; | ||
| import htsjdk.variant.variantcontext.filter.PassingVariantFilter; | ||
| import htsjdk.variant.vcf.VCFHeader; | ||
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| public class VariantContextCollection implements Iterable<VariantContext> { | ||
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| private final TreeSet<VariantContext> variantContexts; | ||
| private final List<StructuralVariant> variants = Lists.newArrayList(); | ||
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| private boolean modified; | ||
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| public VariantContextCollection(@NotNull final VCFHeader header) { | ||
| variantContexts = new TreeSet<>(new VCComparator(header.getSequenceDictionary())); | ||
| } | ||
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| public VariantContextCollection(@NotNull final List<String> contigs) { | ||
| variantContexts = new TreeSet<>(new VCComparator(contigs)); | ||
| } | ||
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| public void add(@NotNull final VariantContext variantContext) { | ||
| modified = true; | ||
| if (variantContext.contains(variantContext)) { | ||
| variantContexts.remove(variantContext); | ||
| variantContexts.add(variantContext); | ||
| } | ||
| } | ||
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| public int remove(@NotNull final Predicate<VariantContext> removePredicate) { | ||
| int removed = 0; | ||
| final Iterator<VariantContext> iterator = variantContexts.iterator(); | ||
| while (iterator.hasNext()) { | ||
| final VariantContext variantContext = iterator.next(); | ||
| if (removePredicate.test(variantContext)) { | ||
| iterator.remove(); | ||
| removed++; | ||
| modified = true; | ||
| } | ||
| } | ||
| return removed; | ||
| } | ||
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| @NotNull | ||
| public List<StructuralVariant> passingVariants() { | ||
| if (modified) { | ||
| modified = false; | ||
| final StructuralVariantFactory factory = new StructuralVariantFactory(new PassingVariantFilter()); | ||
| variantContexts.forEach(factory::addVariantContext); | ||
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| variants.clear(); | ||
| variants.addAll(factory.results()); | ||
| } | ||
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| return variants; | ||
| } | ||
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| @NotNull | ||
| @Override | ||
| public Iterator<VariantContext> iterator() { | ||
| return variantContexts.iterator(); | ||
| } | ||
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| private class VCComparator extends VariantContextComparator { | ||
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| VCComparator(final List<String> contigs) { | ||
| super(contigs); | ||
| } | ||
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| VCComparator(final SAMSequenceDictionary dictionary) { | ||
| super(dictionary); | ||
| } | ||
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| @Override | ||
| public int compare(final VariantContext firstVariantContext, final VariantContext secondVariantContext) { | ||
| int positionResult = super.compare(firstVariantContext, secondVariantContext); | ||
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| return positionResult == 0 ? firstVariantContext.getID().compareTo(secondVariantContext.getID()) : positionResult; | ||
| } | ||
| } | ||
| } |
43 changes: 43 additions & 0 deletions
43
...-estimator/src/test/java/com/hartwig/hmftools/purple/sv/VariantContextCollectionTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| package com.hartwig.hmftools.purple.sv; | ||
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| import static org.junit.Assert.assertEquals; | ||
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| import com.google.common.collect.Lists; | ||
| import com.google.common.collect.Sets; | ||
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| import org.jetbrains.annotations.NotNull; | ||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
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| import htsjdk.variant.vcf.VCFCodec; | ||
| import htsjdk.variant.vcf.VCFHeader; | ||
| import htsjdk.variant.vcf.VCFHeaderVersion; | ||
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| public class VariantContextCollectionTest { | ||
| private static final String SAMPLE = "sample"; | ||
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| private VCFCodec codec; | ||
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| @Before | ||
| public void setup() { | ||
| codec = createTestCodec(); | ||
| } | ||
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| @Test | ||
| public void testAddSetsModifiedFlag() { | ||
| final VariantContextCollection victim = new VariantContextCollection(Lists.newArrayList("1")); | ||
| assertEquals(0, victim.passingVariants().size()); | ||
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| victim.add(codec.decode("1\t192614842\tgridss14_291648b\tT\tTCTCTACACAAG.\t2076.59\tPASS\tSVTYPE=BND\tGT\t./.")); | ||
| assertEquals(1, victim.passingVariants().size()); | ||
| } | ||
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| @NotNull | ||
| private static VCFCodec createTestCodec() { | ||
| VCFCodec codec = new VCFCodec(); | ||
| VCFHeader header = new VCFHeader(Sets.newHashSet(), Sets.newHashSet(SAMPLE)); | ||
| codec.setVCFHeader(header, VCFHeaderVersion.VCF4_2); | ||
| return codec; | ||
| } | ||
| } |