Module Biocaml.Sam

module Sam: Biocaml_sam

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