jlVCF

Very simple VCF file parser module for Julia language.

Sample usage:

vc = VCFIterator("jlVCFtest/somaticsniper.vcf")
while !eof(vc)
    #v is a variable for variant class.
    v = next(vc)
    print(v.POS, v.CHROM)
end

Classes and their fields

See vcf file format specification (https://samtools.github.io/hts-specs/VCFv4.2.pdf) for the detailed explanation of what each field means.

• Variant
  • CHROM::ASCIIString
  • POS::Int64
  • ID::Array{ASCIIString,1}
  • REF::ASCIIString
  • ALT::Array{ASCIIString,1}
  • QUAL
  • FILTER::Array{ASCIIString,1}
  • INFO::Dict{ASCIIString, Any}; keys of this dict are infokey and the values are infovalue.
  • FORMAT::Dict{ASCIIString, Dict{ASCIIString, Any}}. The first layer of keys are sample names, and the second layer keys are fo matkeys.
• VCFIterator
  • version::ASCIIString; version of this VCF file (not functional yet)
  • filename::ASCIIString; name of the source vcf file
  • samples::Array{ASCIIString, 1}; list of sample names
  • contigs::Dict{ASCIIString, Int64}; dict of contigs with contig names as keys and positions as values
  • filters::Dict{ASCIIString, ASCIIString}; dict of filters with filter names as keys and their descriptions as values
  • reference::ASCIIString; reference genome name

Available functions

• VCFIterator related
  • VCFIterator(filename::ASCIIString)
  • getVersion(vc::VCFIterator)
  • getFilename(vc::VCFIterator)
  • getSampleNames(vc::VCFIterator)
  • getINFOProperties(vc::VCFIterator)
  • getFORMATProperties(vc::VCFIterator)
  • getContigs(vc::VCFIterator)
  • getFilters(vc::VCFIterator)
  • getReference(vc::VCFIterator)
  • next(vc::VCFIterator)
  • eof(vc::VCFIterator)
  • close(vc::VCFIterator)
  • reset(vc::VCFIterator)
• Variant related
  • getChrom(v::Variant)
  • getPos(v::Variant)
  • getId(v::Variant)
  • getRef(v::Variant)
  • getAlt(v::Variant)
  • getQual(v::Variant)
  • getFilter(v::Variant)
  • getInfo(v::Variant)
  • getFormat(v::Variant)

Version 0.0.1

CURRENTLY this runs on Julia 0.3.x. Let me know if this needs to be updated.

Naozumi Hiranuma (hiranumn at cs dot washington dot edu) University of Washington Computer Science and Engineering