Module Biocaml_sam

module Biocaml_sam: sig .. end

SAM files.

exception Bad of string

type record_type_code = string

String is exactly three characters, matching the regular expression '@A-Za-zA-Za-z'.

type header_line =

`\|`	`Comment of string`
`\|`	`NonComment of record_type_code * (string * string) list`

type header = header_line list

type alignment = {

`qname : string;`
`flag : int;`
`rname : string;`
`pos : int;`
`mapq : int;`
`cigar : string;`
`rnext : string;`
`pnext : int;`
`tlen : int;`
`seq : string;`
`qual : string;`
`optional : (string * char * string) list;`	`(*`	custom tag-value pairs included beyond required 11	`*)`

}

val record_type_code_of_header_line : header_line -> string

val enum_file : string -> header * alignment Batteries.Enum.t

val header_line_to_string : header_line -> string

val header_to_string : header -> string

val alignment_to_string : alignment -> string