Module Biocaml_sam_deprecated (.ml)

SAM files and SAM-alignements high-level representation.

module Biocaml_sam_deprecated:

sig

Basic Types

Low-Level Items

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.

High-Level Items

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;

}

Definition of a reference sequence.

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

Create a reference sequence.

module Flags:

sig

Manipulate the alignment flags.

type t = private int

Flags are represented as "bit map".

val of_int  : int -> t

val has_multiple_segments  : t -> bool

val each_segment_properly_aligned  : t -> bool

val segment_unmapped  : t -> bool

val next_segment_unmapped  : t -> bool

val seq_is_reverse_complemented  : t -> bool

val next_seq_is_reverse_complemented  : t -> bool

val first_segment  : t -> bool

val last_segment  : t -> bool

val secondary_alignment  : t -> bool

val not_passing_quality_controls  : t -> bool

val pcr_or_optical_duplicate  : t -> bool

include Sexpable.S

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 ]

CIGAR operations.

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

Meta-value used to store "optional content".

type optional_content = (string * char * optional_content_value) list

Alignment optional content.

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 ;

}

High-level representation of a parsed alignment.

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 ]

High-level representation of a parsed entity.

Error Types

module Error:

sig

The possible errors.

type optional_content_parsing = [ `wrong_optional of
 (string * char * string) list *
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_array of
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_type of string ]
 | `wrong_type of string ] ]

Errors which can happen while parsing optional content.

type string_to_raw = [ `incomplete_input of
 Biocaml_internal_utils.Pos.t * string list * string option
 | `invalid_header_tag of Biocaml_internal_utils.Pos.t * string
 | `invalid_tag_value_list of Biocaml_internal_utils.Pos.t * string list
 | `not_an_int of Biocaml_internal_utils.Pos.t * string * string
 | `wrong_alignment of Biocaml_internal_utils.Pos.t * string
 | `wrong_optional_field of Biocaml_internal_utils.Pos.t * string ]

The possible errors one can get while parsing SAM files.

type raw_to_item = [ `comment_after_end_of_header of int * string
 | `duplicate_in_reference_sequence_dictionary of
 Biocaml_sam_deprecated.reference_sequence array
 | `header_after_end_of_header of int * (string * (string * string) list)
 | `header_line_not_first of int
 | `header_line_without_version of (string * string) list
 | `header_line_wrong_sorting of string
 | `missing_ref_sequence_length of (string * string) list
 | `missing_ref_sequence_name of (string * string) list
 | `wrong_cigar_text of string
 | `wrong_flag of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_mapq of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_optional of
 (string * char * string) list *
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_array of
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_type of string ]
 | `wrong_type of string ]
 | `wrong_phred_scores of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_pnext of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_pos of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_qname of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_ref_sequence_length of (string * string) list
 | `wrong_tlen of Biocaml_sam_deprecated.raw_alignment ]

The possible errors one can get while lifting SAM raw_items to higher-level representations. (Note: raw_to_item explicitly contains optional_content_parsing but OCamldoc pastes it inline)

type item_to_raw = [ `wrong_phred_scores of Biocaml_sam_deprecated.alignment ]

The error that may happen while downgrading the higher-level represtation of an alignment.

type parse = [ `comment_after_end_of_header of int * string
 | `duplicate_in_reference_sequence_dictionary of
 Biocaml_sam_deprecated.reference_sequence array
 | `header_after_end_of_header of int * (string * (string * string) list)
 | `header_line_not_first of int
 | `header_line_without_version of (string * string) list
 | `header_line_wrong_sorting of string
 | `incomplete_input of
 Biocaml_internal_utils.Pos.t * string list * string option
 | `invalid_header_tag of Biocaml_internal_utils.Pos.t * string
 | `invalid_tag_value_list of Biocaml_internal_utils.Pos.t * string list
 | `missing_ref_sequence_length of (string * string) list
 | `missing_ref_sequence_name of (string * string) list
 | `not_an_int of Biocaml_internal_utils.Pos.t * string * string
 | `wrong_alignment of Biocaml_internal_utils.Pos.t * string
 | `wrong_cigar_text of string
 | `wrong_flag of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_mapq of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_optional of
 (string * char * string) list *
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_array of
 [ `not_a_char of string
 | `not_a_float of string
 | `not_an_int of string
 | `unknown_type of char
 | `wrong_type of string ]
 | `wrong_type of string ]
 | `wrong_optional_field of Biocaml_internal_utils.Pos.t * string
 | `wrong_phred_scores of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_pnext of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_pos of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_qname of Biocaml_sam_deprecated.raw_alignment 
 | `wrong_ref_sequence_length of (string * string) list
 | `wrong_tlen of Biocaml_sam_deprecated.raw_alignment ]

All possible parsing errors. It is defined as:

   type parse = [

   | string_to_raw

   | raw_to_item

   ]

type t = parse

The union of all possible errors.

S-Expressions conversions for Errors

val optional_content_parsing_of_sexp  : Sexplib.Sexp.t -> optional_content_parsing

val sexp_of_optional_content_parsing  : optional_content_parsing -> Sexplib.Sexp.t

val string_to_raw_of_sexp  : Sexplib.Sexp.t -> string_to_raw

val sexp_of_string_to_raw  : string_to_raw -> Sexplib.Sexp.t

val raw_to_item_of_sexp  : Sexplib.Sexp.t -> raw_to_item

val sexp_of_raw_to_item  : raw_to_item -> Sexplib.Sexp.t

val item_to_raw_of_sexp  : Sexplib.Sexp.t -> item_to_raw

val sexp_of_item_to_raw  : item_to_raw -> Sexplib.Sexp.t

val parse_of_sexp  : Sexplib.Sexp.t -> parse

val sexp_of_parse  : parse -> Sexplib.Sexp.t

val t_of_sexp  : Sexplib.Sexp.t -> parse

val sexp_of_t  : parse -> Sexplib.Sexp.t

end

exception Error of Error.t

The only exception raised by *_exn functions in this module.

Stream functions

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

Parse an input-channel into a stream of high-level items.

val in_channel_to_raw_item_stream  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel ->
 (raw_item, [> Error.parse ])
 Biocaml_internal_utils.Result.t Biocaml_internal_utils.Stream.t

Parse an input-channel into a stream of low-level ("raw") items.

val in_channel_to_item_stream_exn  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel ->
 item Biocaml_internal_utils.Stream.t

Like in_channel_to_item_stream but each call to Stream.next may raise Error _

val in_channel_to_raw_item_stream_exn  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel ->
 raw_item Biocaml_internal_utils.Stream.t

Like in_channel_to_raw_item_stream but each call to Stream.next may raise Error _

Low-level partial parsing

Here we expose functions used both in Biocaml_sam.Transform and Biocaml_bam.Transform for parsing. It can be ignored by most users but can be useful.

val parse_cigar_text  : string ->
 (cigar_op array, [> `wrong_cigar_text of string ])
 Biocaml_internal_utils.Result.t

Parse CIGAR operations from a string.

val parse_optional_content  : (string * char * string) list ->
 (optional_content,
 [> Error.optional_content_parsing ])
 Biocaml_internal_utils.Result.t

Parse optional content from a "tokenized" string.

val parse_header_line  : 'a ->
 string ->
 ([> `comment of string | `header of string * (string * string) list ],
 [> `invalid_header_tag of 'a * string
 | `invalid_tag_value_list of 'a * string list ])
 Biocaml_internal_utils.Result.t

Parse a header line form a string. The first argument is used to pass the location to the error values (c.f. Biocaml_sam_deprecated.Error.string_to_raw).

val expand_header_line  : (string * string) list ->
 ([> `header_line of
 string * [ `coordinate | `queryname | `unknown | `unsorted ] *
 (string * string) list ],
 [> `header_line_without_version of (string * string) list
 | `header_line_wrong_sorting of string ])
 Biocaml_internal_utils.Result.t

Parse a header line into a more detailed type.

Low-level Transforms

module Transform:

sig

Low-level, threading-model agnostic transforms (c.f. Biocaml_transform).

val string_to_raw  : ?filename:string ->
 unit ->
 (string,
 (Biocaml_sam_deprecated.raw_item,
 [> Biocaml_sam_deprecated.Error.string_to_raw ])
 Biocaml_internal_utils.Result.t)
 Biocaml_transform.t

Create a parsing "stoppable" transform.

val raw_to_string  : unit -> (Biocaml_sam_deprecated.raw_item, string) Biocaml_transform.t

Create a printing "stoppable" transform.

val raw_to_item  : unit ->
 (Biocaml_sam_deprecated.raw_item,
 (Biocaml_sam_deprecated.item, [> Biocaml_sam_deprecated.Error.raw_to_item ])
 Biocaml_internal_utils.Result.t)
 Biocaml_transform.t

Create a transform that lifts raw_items to items

val item_to_raw  : unit ->
 (Biocaml_sam_deprecated.item,
 (Biocaml_sam_deprecated.raw_item,
 [> Biocaml_sam_deprecated.Error.item_to_raw ])
 Biocaml_internal_utils.Result.t)
 Biocaml_transform.t

Create a transform that downgrades items to raw_items

end

S-Expressions

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 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 sexp_of_item  : item -> Sexplib.Sexp.t

end