Variant and Genotype converters will need VCF header

[heuermh]

No description provided.

[akmorrow13]

This would look something like this:

val codec = new VCFCodec()

val vcfReader: AbstractFeatureReader[HtsjdkVariantContext, LineIterator] = AbstractFeatureReader.getFeatureReader(filename, codec)


val header: VCFHeader = vcfReader.getHeader().asInstanceOf[VCFHeader]

val converter = new VariantContextConverter(
      getHeaderLines(header),
      ValidationStringency.LENIENT, false)


  // defined in ADAM in VariantContextConverter line 266
def getHeaderLines(header: VCFHeader): Seq[VCFHeaderLine] = {
    (header.getFilterLines ++
      header.getFormatHeaderLines ++
      header.getInfoHeaderLines ++
      header.getOtherHeaderLines).toSeq
  }

[heuermh]

Yeah, but note the standard headers that ADAM uses are not exactly the same as the standard headers in htsjdk, because they don't actually follow the VCF specification.

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala#L191