/ 
VCF-1.003
River stage zero No dependents
/ VCF::V4_0

VCFv4.0

VCFv4.0 specific functions

parse_header_line

Usage   : $vcf->parse_header_line(q[##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">])
          $vcf->parse_header_line(q[reference=1000GenomesPilot-NCBI36])
Args    :
Returns :

fill_ref_alt_mapping

About   : A tool for merging VCFv4.0 records. The subroutine unifies the REFs and creates a mapping
            from the original haplotypes to the haplotypes based on the new REF. Consider the following
            example:
                REF ALT
                G    GA
                GT   G
                GT   GA
                GT   GAA
                GTC  G
                G    <DEL>
            my $map={G=>{GA=>1},GT=>{G=>1,GA=>1,GAA=>1},GTC=>{G=>1},G=>{'<DEL>'=>1}};
            my $new_ref=$vcf->fill_ref_alt_mapping($map);

          The call returns GTC and $map is now
                G    GA     ->      GTC  GATC
                GT   G      ->      GTC  GC
                GT   GA     ->      GTC  GAC
                GT   GAA    ->      GTC  GAAC
                GTC  G      ->      GTC  G
                G    <DEL>  ->      GTC  <DEL>
Args    :
Returns : New REF string and fills the hash with appropriate ALT or undef on error.

normalize_alleles

About   : Makes REF and ALT alleles more compact if possible (e.g. TA,TAA -> T,TA)
Usage   : my $line = $vcf->next_data_array();
          ($ref,@alts) = $vcf->normalize_alleles($$line[3],$$line[4]);