Previous Up Next

Module Biocaml_sam (.ml)

module Biocaml_sam: sig .. end

SAM files.

type raw_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;

}

The contents of an alignment line.

type raw_item = [ `alignment of raw_alignment 
 | `comment of string
 | `header of string * (string * string) list ]

The "items" of a parsed SAM file stream.

type reference_sequence = {

ref_name :string;

ref_length :int;

ref_assembly_identifier :string option;

ref_checksum :string option;

ref_species :string option;

ref_uri :string option;

ref_unknown :(string * string) list;

}

val reference_sequence  : ?assembly_identifier:string ->
 ?checksum:string ->
 ?species:string ->
 ?uri:string ->
 ?unknown_data:(string * string) list ->
 string -> int -> reference_sequence

module Flags: sig .. end

type cigar_op = [ `D of int
 | `Eq of int
 | `H of int
 | `I of int
 | `M of int
 | `N of int
 | `P of int
 | `S of int
 | `X of int ]

type optional_content_value = [ `array of char * optional_content_value array
 | `char of char
 | `float of float
 | `int of int
 | `string of string ]

type optional_content = (string * char * optional_content_value) list

type alignment = {

query_template_name :string;

flags :Flags.t ;

reference_sequence :[ `name of string
 | `none
 | `reference_sequence of reference_sequence ];

position :int option;

mapping_quality :int option;

cigar_operations :cigar_op array;

next_reference_sequence :[ `name of string
 | `none
 | `qname
 | `reference_sequence of reference_sequence ];

next_position :int option;

template_length :int option;

sequence :[ `none | `reference | `string of string ];

quality :Biocaml_phred_score.t array;

optional_content :optional_content ;

}

type item = [ `alignment of alignment 
 | `comment of string
 | `header of string * (string * string) list
 | `header_line of
 string * [ `coordinate | `queryname | `unknown | `unsorted ] *
 (string * string) list
 | `reference_sequence_dictionary of reference_sequence array ]

module Error: sig .. end

val in_channel_to_item_stream  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel ->
 (item, Error.parse) Core.Result.t Stream.t

module Low_level_parsing: sig .. end

module Transform: sig .. end

val raw_alignment_of_sexp  : Sexplib.Sexp.t -> raw_alignment

val sexp_of_raw_alignment  : raw_alignment -> Sexplib.Sexp.t

The contents of an alignment line.

val raw_item_of_sexp  : Sexplib.Sexp.t -> raw_item

val raw_item_of_sexp__  : Sexplib.Sexp.t -> raw_item

val sexp_of_raw_item  : raw_item -> Sexplib.Sexp.t

The "items" of a parsed SAM file stream.

val reference_sequence_of_sexp  : Sexplib.Sexp.t -> reference_sequence

val sexp_of_reference_sequence  : reference_sequence -> Sexplib.Sexp.t

val cigar_op_of_sexp  : Sexplib.Sexp.t -> cigar_op

val cigar_op_of_sexp__  : Sexplib.Sexp.t -> cigar_op

val sexp_of_cigar_op  : cigar_op -> Sexplib.Sexp.t

val optional_content_value_of_sexp  : Sexplib.Sexp.t -> optional_content_value

val optional_content_value_of_sexp__  : Sexplib.Sexp.t -> optional_content_value

val sexp_of_optional_content_value  : optional_content_value -> Sexplib.Sexp.t

val optional_content_of_sexp  : Sexplib.Sexp.t -> optional_content

val sexp_of_optional_content  : optional_content -> Sexplib.Sexp.t

val alignment_of_sexp  : Sexplib.Sexp.t -> alignment

val sexp_of_alignment  : alignment -> Sexplib.Sexp.t

val item_of_sexp  : Sexplib.Sexp.t -> item

val item_of_sexp__  : Sexplib.Sexp.t -> item

val sexp_of_item  : item -> Sexplib.Sexp.t

The possible errors one can get while parsing SAM files.

Create a parsing "stoppable" transform.

Create a printing "stoppable" transform.