Parsing of VCF files.
This module implements VCFv4.1, as defined by 1000 genomes project: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
Types, allowed for VCF FORMAT meta header.
Types, allowed for VCF INFO meta header.
type vcf_meta = {vcfm_version : string;vcfm_id_cache : vcf_id Core_kernel.Set.Poly.t;vcfm_info : (vcf_id, vcf_info_meta) Core_kernel.Hashtbl.t;vcfm_filters : (vcf_id * vcf_filter_meta) list;vcfm_format : (vcf_id, vcf_format_meta) Core_kernel.Hashtbl.t;vcfm_alt : (string, vcf_alt_meta) Core_kernel.Hashtbl.t;vcfm_arbitrary : (string, string) Core_kernel.Hashtbl.t;vcfm_header : string list;vcfm_samples : string list;}type vcf_row = {vcfr_chrom : string;vcfr_pos : int;vcfr_ids : string list;vcfr_ref : string;vcfr_alts : string list;vcfr_qual : float option;vcfr_filter : vcf_id list;vcfr_info : (vcf_id, vcf_info list) Core_kernel.Hashtbl.t;vcfr_samples : (vcf_id, (vcf_id * vcf_format list) list) Core_kernel.Hashtbl.t;}type item = vcf_rowtype vcf_parse_row_error = [ | `invalid_int of string| `invalid_float of string| `info_type_coersion_failure of vcf_info_type * string| `format_type_coersion_failure of vcf_format_type * string| `invalid_dna of string| `unknown_info of vcf_id| `unknown_filter of vcf_id| `unknown_alt of string| `duplicate_ids of vcf_id list| `invalid_arguments_length of vcf_id * int * int| `invalid_row_length of int * int| `malformed_sample of string| `unknown_format of vcf_id ]type vcf_parse_error = [ | `malformed_meta of Pos.t * string| `malformed_row of Pos.t * vcf_parse_row_error * string| `malformed_header of Pos.t * string| `incomplete_input of Pos.t * string list * string option| `not_ready ]val parse_error_to_string : vcf_parse_error -> stringmodule Transform : sig ... end