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Module Biocaml_bam (.ml)

Parsing and printing of BAM files.

module Biocaml_bam:
sig

This module provides parsing from string buffers to raw_items (minimal parsing), and conversion from raw_items to Sam.items (higher-level constructs).

Item Types


type raw_alignment = {
   qname : string;
   flag : int;
   ref_id : int;
   pos : int; (*Positions are 0-based, -1 if undefined*)
   mapq : int;
   bin : int;
   cigar : string;
   next_ref_id : int;
   pnext : int;
   tlen : int;
   seq : string;
   qual : int array;
   optional : string;
}
The type of an alignment record in a BAM file.

The rather meaningless names come from the “almost official” specification of the format (c.f. SAM1.pdf).

type raw_item = [ `alignment of raw_alignment
       | `header of string
       | `reference_information of (string * int) array ]
The different kinds of items one can get from parsing a BAM file.

Error Types


module Error:
sig

The possible errors returned by parsing and printing functions.
type raw_bam = [ `read_name_not_null_terminated of string
       | `reference_information_name_not_null_terminated of string
       | `reference_information_overflow of int * string
       | `wrong_int32 of string
       | `wrong_magic_number of string ]
The possible non-gzip-related errors encountered while parsing a BAM file.
type parse_optional = [ `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string ]
The potential failures while parsing the optional content in BAM alignments.
type parse_cigar = [ `wrong_cigar of string | `wrong_cigar_length of int ]
The potential failures while parsing the so-called CIGAR operations
type raw_to_item = [ `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `invalid_header_tag of int * string
       | `invalid_tag_value_list of int * string list
       | `reference_sequence_not_found of Biocaml_bam.raw_alignment
       | `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string
       | `wrong_cigar of string
       | `wrong_cigar_length of int
       | `wrong_flag of Biocaml_bam.raw_alignment
       | `wrong_mapq of Biocaml_bam.raw_alignment
       | `wrong_pnext of Biocaml_bam.raw_alignment
       | `wrong_pos of Biocaml_bam.raw_alignment
       | `wrong_qname of Biocaml_bam.raw_alignment
       | `wrong_tlen of Biocaml_bam.raw_alignment ]
All the possible errors one can encounter while going from raw_items to Sam.items.
type item_to_raw = [ `cannot_get_sequence of Biocaml_sam_deprecated.alignment
       | `header_item_not_first of string
       | `reference_name_not_found of Biocaml_sam_deprecated.alignment * string ]
Inconsistency errors that may happen while trnasforming a Sam.item to a raw_item.
type t = [ `cannot_get_sequence of Biocaml_sam_deprecated.alignment
       | `header_item_not_first of string
       | `header_line_not_first of int
       | `header_line_without_version of (string * string) list
       | `header_line_wrong_sorting of string
       | `invalid_header_tag of int * string
       | `invalid_tag_value_list of int * string list
       | `read_name_not_null_terminated of string
       | `reference_information_name_not_null_terminated of string
       | `reference_information_overflow of int * string
       | `reference_name_not_found of Biocaml_sam_deprecated.alignment * string
       | `reference_sequence_not_found of Biocaml_bam.raw_alignment
       | `wrong_auxiliary_data of
           [ `array_size of int
           | `null_terminated_hexarray
           | `null_terminated_string
           | `out_of_bounds
           | `unknown_type of char
           | `wrong_int32 of string ] * string
       | `wrong_cigar of string
       | `wrong_cigar_length of int
       | `wrong_flag of Biocaml_bam.raw_alignment
       | `wrong_int32 of string
       | `wrong_magic_number of string
       | `wrong_mapq of Biocaml_bam.raw_alignment
       | `wrong_pnext of Biocaml_bam.raw_alignment
       | `wrong_pos of Biocaml_bam.raw_alignment
       | `wrong_qname of Biocaml_bam.raw_alignment
       | `wrong_tlen of Biocaml_bam.raw_alignment ]
The union of all the errors.
val raw_bam_of_sexp : Sexplib.Sexp.t -> raw_bam
val sexp_of_raw_bam : raw_bam -> Sexplib.Sexp.t
val parse_optional_of_sexp : Sexplib.Sexp.t -> parse_optional
val sexp_of_parse_optional : parse_optional -> Sexplib.Sexp.t
val parse_cigar_of_sexp : Sexplib.Sexp.t -> parse_cigar
val sexp_of_parse_cigar : parse_cigar -> 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 t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end

In_channel Functions


exception Error of [ `bam of Error.t | `unzip of Biocaml_zip.Error.unzip ]
The exception thrown by *_exn functions in this module.
val in_channel_to_raw_item_stream : ?zlib_buffer_size:int ->
       ?buffer_size:int ->
       Pervasives.in_channel ->
       (raw_item,
        [> `bam of [> Error.raw_bam ]
         | `unzip of [> Biocaml_zip.Error.unzip ] ])
       Core.Std.Result.t Stream.t
Create a stream of raw_item results from an input-channel.
val in_channel_to_raw_item_stream_exn : ?zlib_buffer_size:int ->
       ?buffer_size:int -> Pervasives.in_channel -> raw_item Stream.t
Create a stream of raw_items from an input-channel (any call to Stream.next may throw an Error _ exception).
val in_channel_to_item_stream : ?zlib_buffer_size:int ->
       ?buffer_size:int ->
       Pervasives.in_channel ->
       (Biocaml_sam_deprecated.item,
        [> `bam of [> Error.t ] | `unzip of [> Biocaml_zip.Error.unzip ] ])
       Core.Std.Result.t Stream.t
Create a stream of full Sam.item results from an input-channel.
val in_channel_to_item_stream_exn : ?zlib_buffer_size:int ->
       ?buffer_size:int ->
       Pervasives.in_channel -> Biocaml_sam_deprecated.item Stream.t
Create a stream of Sam.items from an input-channel (any call to Stream.next may throw an Error _ exception).

Transform.t Creations 


module Transform:
sig

The low-level Transform.t implementations.
val raw_to_item : unit ->
       (Biocaml_bam.raw_item,
        (Biocaml_sam_deprecated.item, [> Biocaml_bam.Error.raw_to_item ])
        Core.Std.Result.t)
       Biocaml_transform.t
Create a transform that lifts raw_items to the higher-level representation defined in the Biocaml_sam module.
val string_to_raw : ?zlib_buffer_size:int ->
       unit ->
       (string,
        (Biocaml_bam.raw_item,
         [> `bam of Biocaml_bam.Error.raw_bam | `unzip of Biocaml_zip.Error.unzip ])
        Core.Std.Result.t)
       Biocaml_transform.t
Create a transform that parses a BAM file. The zlib_buffer_size is passed to the Biocaml_zip module.
val item_to_raw : unit ->
       (Biocaml_sam_deprecated.item,
        (Biocaml_bam.raw_item, [> Biocaml_bam.Error.item_to_raw ]) Core.Std.Result.t)
       Biocaml_transform.t
Create a transform that downgrades Sam.items to raw_items.
val raw_to_string : ?gzip_level:int ->
       ?zlib_buffer_size:int ->
       unit -> (Biocaml_bam.raw_item, string) Biocaml_transform.t
Create a transform that “prints” raw_items in the BAM format. The gzip_level and zlib_buffer_size options are passed to the Biocaml_zip module.
end

Lower-level (parsing) functions


val parse_cigar : ?pos:int ->
       ?len:int ->
       string ->
       (Biocaml_sam_deprecated.cigar_op array, [> Error.parse_cigar ])
       Core.Std.Result.t
Parse CIGAR operations from a string (c.f. raw_alignment.cigar).
val parse_optional : ?pos:int ->
       ?len:int ->
       string ->
       (Biocaml_sam_deprecated.optional_content,
        [> Error.parse_optional ])
       Core.Std.Result.t
Parse optional content from a string (c.f. raw_alignment.optional).

S-Expressions


val raw_alignment_of_sexp : Sexplib.Sexp.t -> raw_alignment
val sexp_of_raw_alignment : raw_alignment -> Sexplib.Sexp.t
val raw_item_of_sexp : Sexplib.Sexp.t -> raw_item
val sexp_of_raw_item : raw_item -> Sexplib.Sexp.t
end