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Module Biocaml_vcf (.ml)

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

module Biocaml_vcf:
sig
type vcf_id = string 
type vcf_description = string 
type vcf_number =
| Number of int
| OnePerAllele
| OnePerGenotype
| Unknown 
type vcf_format_type = [ `character_value | `float_value | `integer_value | `string_value ]
Types, allowed for VCF FORMAT meta header.
type vcf_info_type = [ `character_value
       | `flag_value
       | `float_value
       | `integer_value
       | `string_value ]
Types, allowed for VCF INFO meta header.
type vcf_info_meta =
| Info of vcf_number * vcf_info_type
* vcf_description		 
type vcf_filter_meta =
| Filter of vcf_description 
type vcf_format_meta =
| Format of vcf_number * vcf_format_type
* vcf_description		 
type vcf_alt_meta =
| Alt of vcf_description 
type vcf_meta = {
   vcfm_version : string;
   vcfm_id_cache : vcf_id Biocaml_internal_pervasives.Set.Poly.t;
   vcfm_info : (vcf_id, vcf_info_meta)
Biocaml_internal_pervasives.Hashtbl.t;
   vcfm_filters : (vcf_id * vcf_filter_meta) list;
   vcfm_format : (vcf_id, vcf_format_meta)
Biocaml_internal_pervasives.Hashtbl.t;
   vcfm_alt : (string, vcf_alt_meta) Biocaml_internal_pervasives.Hashtbl.t;
   vcfm_arbitrary : (string, string) Biocaml_internal_pervasives.Hashtbl.t;
   vcfm_header : string list;
   vcfm_samples : string list;
} 
type vcf_format = [ `character of char
       | `float of float
       | `integer of int
       | `missing
       | `string of string ] 
type vcf_info = [ `character of char
       | `flag of string
       | `float of float
       | `integer of int
       | `missing
       | `string of string ] 
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)
Biocaml_internal_pervasives.Hashtbl.t;
   vcfr_samples : (vcf_id, (vcf_id * vcf_format list) list)
Biocaml_internal_pervasives.Hashtbl.t;
} 
type item = vcf_row 

module Pos: module type of Biocaml_pos
type vcf_parse_row_error = [ `duplicate_ids of vcf_id list
       | `format_type_coersion_failure of vcf_format_type * string
       | `info_type_coersion_failure of vcf_info_type * string
       | `invalid_arguments_length of vcf_id * int * int
       | `invalid_dna of string
       | `invalid_float of string
       | `invalid_int of string
       | `invalid_row_length of int * int
       | `malformed_sample of string
       | `unknown_alt of string
       | `unknown_filter of vcf_id
       | `unknown_format of vcf_id
       | `unknown_info of vcf_id ] 
type vcf_parse_error = [ `incomplete_input of Pos.t * string list * string option
       | `malformed_header of Pos.t * string
       | `malformed_meta of Pos.t * string
       | `malformed_row of
           Pos.t * vcf_parse_row_error * string
       | `not_ready ] 
val parse_error_to_string : vcf_parse_error -> string

module Transform:
sig
val string_to_item : ?filename:string ->
       unit ->
       (string, (Biocaml_vcf.item, Biocaml_vcf.vcf_parse_error) Core.Result.t)
       Biocaml_transform.t
end
end