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(SV) Overhaul tests on assembly-based non-complex breakpoint and type…
… inference code Also * expand cases on BND format variants * change to how VariantContext are extracted from NARL and SVType * refactor the tool DiscoverVariantsFromContigAlignmentsSAMSpark into a new worker class ContigChimericAlignmentIterativeInterpreter
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344 changes: 152 additions & 192 deletions
344
...java/org/broadinstitute/hellbender/tools/spark/sv/discovery/AnnotatedVariantProducer.java
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361 changes: 217 additions & 144 deletions
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...main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/BreakEndVariantType.java
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267 changes: 18 additions & 249 deletions
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...ute/hellbender/tools/spark/sv/discovery/DiscoverVariantsFromContigAlignmentsSAMSpark.java
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213 changes: 157 additions & 56 deletions
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src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SimpleSVType.java
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152 changes: 140 additions & 12 deletions
152
src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/SvType.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,41 +1,169 @@ | ||
| package org.broadinstitute.hellbender.tools.spark.sv.discovery; | ||
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| import htsjdk.variant.variantcontext.Allele; | ||
| import htsjdk.variant.variantcontext.VariantContextBuilder; | ||
| import htsjdk.variant.vcf.VCFConstants; | ||
| import org.apache.commons.lang3.EnumUtils; | ||
| import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource; | ||
| import org.broadinstitute.hellbender.exceptions.GATKException; | ||
| import org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype; | ||
| import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants; | ||
| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
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| import java.util.Collections; | ||
| import java.util.Map; | ||
| import java.io.IOException; | ||
| import java.util.*; | ||
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| import static org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.INTERVAL_VARIANT_ID_FIELD_SEPARATOR; | ||
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| /** | ||
| * Various types of structural variations | ||
| * Various types of structural variations. | ||
| * Holding minimum information on VariantContext | ||
| * it can hold: | ||
| * CHR, POS, ID, REF, ALT, SVTYPE, END (optional), SVLEN(optional) | ||
| */ | ||
| public abstract class SvType { | ||
| public static final int NO_APPLICABLE_END = -1; | ||
| public static final int NO_APPLICABLE_LEN = -1; | ||
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| // fields whose name starts with "variant" are following the VCF spec, i.e. they can be used directly to construct VariantContextBuilder | ||
| protected final String variantChromosome; | ||
| protected final int variantStart; | ||
| protected final int variantStop; | ||
| protected final String variantId; | ||
| protected final Allele refAllele; | ||
| protected final Allele altAllele; | ||
| protected final int svLen; | ||
| protected final Map<String, String> extraAttributes; | ||
| protected final Map<String, Object> typeSpecificAttributes; | ||
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| protected static final Map<String, String> noExtraAttributes = Collections.emptyMap(); | ||
| protected static final Map<String, Object> noExtraAttributes = Collections.emptyMap(); | ||
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| protected SvType(final String id, final Allele altAllele, final int len, final Map<String, String> typeSpecificExtraAttributes) { | ||
| variantId = id; | ||
| public SvType(final String variantChromosome, final int variantStart, final int variantStop, final String variantId, | ||
| final Allele refAllele, final Allele altAllele, final int svLen, final Map<String, Object> typeSpecificAttributes) { | ||
| this.variantChromosome = variantChromosome; | ||
| this.variantStart = variantStart; | ||
| this.variantStop = variantStop; | ||
| this.variantId = variantId; | ||
| this.refAllele = refAllele; | ||
| this.altAllele = altAllele; | ||
| svLen = len; | ||
| extraAttributes = typeSpecificExtraAttributes; | ||
| this.svLen = svLen; | ||
| this.typeSpecificAttributes = typeSpecificAttributes; | ||
| } | ||
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| public final VariantContextBuilder getBasicInformation() { | ||
| if ( ! hasApplicableEnd() ) { | ||
| VariantContextBuilder builder = new VariantContextBuilder() | ||
| .chr(variantChromosome).start(variantStart).stop(variantStart) | ||
| .id(variantId) | ||
| .alleles(new ArrayList<>(Arrays.asList(refAllele, altAllele))) | ||
| .attribute(GATKSVVCFConstants.SVTYPE, toString()); | ||
| typeSpecificAttributes.forEach(builder::attribute); | ||
| return builder; | ||
| } else { // assuming if there's valid END, there must be valid SVLEN | ||
| VariantContextBuilder builder = new VariantContextBuilder() | ||
| .chr(variantChromosome).start(variantStart).stop(variantStop) | ||
| .id(variantId) | ||
| .alleles(new ArrayList<>(Arrays.asList(refAllele, altAllele))) | ||
| .attribute(VCFConstants.END_KEY, variantStop) | ||
| .attribute(GATKSVVCFConstants.SVTYPE, toString()) | ||
| .attribute(GATKSVVCFConstants.SVLEN, svLen); | ||
| typeSpecificAttributes.forEach(builder::attribute); | ||
| return builder; | ||
| } | ||
| } | ||
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| public String getVariantChromosome() { | ||
| return variantChromosome; | ||
| } | ||
| public int getVariantStart() { | ||
| return variantStart; | ||
| } | ||
| public int getVariantStop() { | ||
| return variantStop; | ||
| } | ||
| public final String getInternalVariantId() { | ||
| return variantId; | ||
| } | ||
| Allele getRefAllele() { | ||
| return refAllele; | ||
| } | ||
| public final Allele getAltAllele() { | ||
| return altAllele; | ||
| } | ||
| public final int getSVLength() { | ||
| return svLen; | ||
| } | ||
| public final Map<String, String> getTypeSpecificAttributes() { | ||
| return extraAttributes; | ||
| public final Map<String, Object> getTypeSpecificAttributes() { | ||
| return typeSpecificAttributes; | ||
| } | ||
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| public abstract boolean hasApplicableEnd(); | ||
| public abstract boolean hasApplicableLength(); | ||
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| @Override | ||
| public boolean equals(final Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
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| final SvType svType = (SvType) o; | ||
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| if (svLen != svType.svLen) return false; | ||
| if (!variantId.equals(svType.variantId)) return false; | ||
| if (!altAllele.equals(svType.altAllele)) return false; | ||
| if (typeSpecificAttributes.size() != svType.typeSpecificAttributes.size()) return false; | ||
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| for ( final Map.Entry<String, Object> act : typeSpecificAttributes.entrySet() ) { | ||
| if ( svType.typeSpecificAttributes.containsKey(act.getKey())) { | ||
| if ( ! act.getValue().equals(svType.typeSpecificAttributes.get(act.getKey()))) | ||
| return false; | ||
| } else | ||
| return false; | ||
| } | ||
| return true; | ||
| } | ||
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| @Override | ||
| public int hashCode() { | ||
| int result = variantId.hashCode(); | ||
| result = 31 * result + altAllele.hashCode(); | ||
| result = 31 * result + svLen; | ||
| result = 31 * result + typeSpecificAttributes.hashCode(); | ||
| return result; | ||
| } | ||
|
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| // TODO: 5/23/18 any better way to do this? | ||
| public static SortedSet<String> getKnownTypes() { | ||
| final SortedSet<String> knownTypes = new TreeSet<>( EnumUtils.getEnumMap(SimpleSVType.SupportedType.class).keySet() ); | ||
|
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| knownTypes.add(GATKSVVCFConstants.CPX_SV_SYB_ALT_ALLELE_STR); | ||
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| for (final BreakEndVariantType.SupportedType supportedType : BreakEndVariantType.SupportedType.values()) { | ||
| knownTypes.add(supportedType.name()); | ||
| } | ||
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| return Collections.unmodifiableSortedSet(knownTypes); | ||
| } | ||
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| public static String makeLocationString(final String chr1, final int pos1, final String chr2, final int pos2) { | ||
| return chr1 + INTERVAL_VARIANT_ID_FIELD_SEPARATOR | ||
| + pos1 + INTERVAL_VARIANT_ID_FIELD_SEPARATOR | ||
| + (chr2.equals(chr1) ? "" : chr2 + INTERVAL_VARIANT_ID_FIELD_SEPARATOR) | ||
| + pos2; | ||
| } | ||
|
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| public static String makeLocationString(final NovelAdjacencyAndAltHaplotype novelAdjacencyAndAltHaplotype) { | ||
| String leftContig = novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getContig(); | ||
| String rightContig = novelAdjacencyAndAltHaplotype.getLeftJustifiedRightRefLoc().getContig(); | ||
| int pos1 = novelAdjacencyAndAltHaplotype.getLeftJustifiedLeftRefLoc().getStart(); | ||
| int pos2 = novelAdjacencyAndAltHaplotype.getLeftJustifiedRightRefLoc().getEnd(); | ||
| return makeLocationString(leftContig, pos1, rightContig, pos2); | ||
| } | ||
|
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| static byte[] extractRefBases(final SimpleInterval interval, final ReferenceMultiSource reference) { | ||
| try { | ||
| return reference.getReferenceBases(interval).getBases(); | ||
| } catch (final IOException ioex) { | ||
| throw new GATKException("Failed to extract bases from region: " + interval.toString()); | ||
| } | ||
| } | ||
| public abstract boolean isBreakEndOnly(); | ||
| } |
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