Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Populate fields on VariantAnnotation #1283

Closed
wants to merge 1 commit into from
Closed

Populate fields on VariantAnnotation #1283

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
57 changes: 54 additions & 3 deletions adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -412,11 +412,62 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
*/
private def extractVariantAnnotation(variant: Variant,
vc: HtsjdkVariantContext): VariantAnnotation = {
val annotation = VariantAnnotation.newBuilder()
val vab = VariantAnnotation.newBuilder()
.setVariant(variant)
.build

VariantAnnotationConverter.convert(vc, annotation)
// Number=0, Number=1, Number=N, Number=. VCF INFO reserved keys shared
// across all alternate alleles in the same VCF record
Option(vc.getAttributeAsString("AA", null)).foreach(vab.setAncestralAllele(_))
Option(vc.getAttribute("DB").asInstanceOf[java.lang.Boolean]).foreach(vab.setDbSnp(_))
Option(vc.getAttribute("H2").asInstanceOf[java.lang.Boolean]).foreach(vab.setHapMap2(_))
Option(vc.getAttribute("H3").asInstanceOf[java.lang.Boolean]).foreach(vab.setHapMap2(_))
Option(vc.getAttribute("VALIDATED").asInstanceOf[java.lang.Boolean]).foreach(vab.setValidated(_))
Option(vc.getAttribute("1000G").asInstanceOf[java.lang.Boolean]).foreach(vab.setThousandGenomes(_))

val index = vc.getAlternateAlleles.indexOf(variant.getAlternateAllele)

// Number=A VCF INFO reserved keys split for multi-allelic sites by index
val ac = vc.getAttributeAsList("AC")
if (ac.size > index) {
vab.setAlleleCount(ac.get(index).asInstanceOf[java.lang.Integer])
}

val af = vc.getAttributeAsList("AF")
if (af.size > index) {
vab.setAlleleFrequency(af.get(index).asInstanceOf[java.lang.Float])
}

val cigar = vc.getAttributeAsList("CIGAR")
if (cigar.size > index) {
vab.setCigar(cigar.get(index).asInstanceOf[java.lang.String])
}

// Number=R VCF INFO reserved keys split for multi-allelic sites by index + 1
val ad = vc.getAttributeAsList("AD")
if (ad.size > (index + 1)) {
vab.setReadDepth(ad.get(index + 1).asInstanceOf[java.lang.Integer])
}

val adf = vc.getAttributeAsList("ADF")
if (adf.size > (index + 1)) {
vab.setForwardReadDepth(adf.get(index + 1).asInstanceOf[java.lang.Integer])
}

val adr = vc.getAttributeAsList("ADR")
if (adr.size > (index + 1)) {
vab.setReverseReadDepth(adr.get(index + 1).asInstanceOf[java.lang.Integer])
}

// Number=. VCF INFO key ANN split for multi-allelic sites by alternate allele
TranscriptEffectConverter.convertToTranscriptEffects(variant, vc).foreach(vab.setTranscriptEffects(_))

// for all VCF INFO header lines {
// if Number=0, 1, n, . share across all alternate alleles in the same VCF record
// if Number=A split for multi-allelic sites by index
// if Number=R split for multi-allelic sites by index + 1
// }

VariantAnnotationConverter.convert(vc, vab.build)
}

/**
Expand Down