Previous  Up  Next

Module Biocaml_bam_alt (.ml)

Read and write BAM format.

The implementation does its best to comply with the official specification.

module Biocaml_bam_alt:
sig

A BAM file is composed of a header and a list of alignment records. The datatypes used in this module are based on those defined in the Biocaml.SAM module.

BAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.

module Header:
sig
type t 
val of_sam : Biocaml_sam.header -> t
val to_sam : t -> Biocaml_sam.header
end
type alignment = Biocaml_sam.alignment

Representation of partially parsed alignments. When traversing a BAM file for a specific calculation, it may be that only some fields of the alignment records are actually used. In that case, it can be significantly faster to use this representation. As a downside, some encoding errors in the BAM file can go unnoticed.

module Alignment0:
sig
type t 
val qname : t -> string option
val flags : t -> Biocaml_sam.Flags.t Core.Std.Or_error.t
val rname : t ->
       Biocaml_bam_alt.Header.t -> string option Core.Std.Or_error.t
val pos : t -> int option
val mapq : t -> int option
val cigar : t -> Biocaml_sam.cigar_op list Core.Std.Or_error.t
val rnext : t ->
       Biocaml_bam_alt.Header.t -> Biocaml_sam.rnext option Core.Std.Or_error.t
val pnext : t -> int option
val tlen : t -> int option
val seq : t -> string option
val qual : t ->
       Biocaml_phred_score.t list Core.Std.Or_error.t
val optional_fields : t ->
       Biocaml_sam.optional_field list Core.Std.Or_error.t
val decode : t ->
       Biocaml_bam_alt.Header.t -> Biocaml_bam_alt.alignment Core.Std.Or_error.t
val encode : Biocaml_bam_alt.alignment ->
       Biocaml_bam_alt.Header.t -> t Core.Std.Or_error.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end
val read0 : Pervasives.in_channel ->
       (Header.t *
        Alignment0.t Core.Std.Or_error.t Stream.t)
       Core.Std.Or_error.t
read0 ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored (partially parsed) alignments. The stream stops after the first error.
val with_file0 : string ->
       f:(Header.t ->
          Alignment0.t Core.Std.Or_error.t Stream.t ->
          'a Core.Std.Or_error.t) ->
       'a Core.Std.Or_error.t
with_file fn ~f opens a BAM file for reading, applies f and closes the file after that, even if f raises an exception. Beware: the result of f should not lazily depend on the stream it receives as a second argument, since after the call to with_file the underlying channel is closed.
val write0 : Header.t ->
       Alignment0.t Stream.t -> Pervasives.out_channel -> unit
write0 h xs oc writes the header h and (partially parsed) alignments xs to oc.
val read : Pervasives.in_channel ->
       (Header.t *
        alignment Core.Std.Or_error.t Stream.t)
       Core.Std.Or_error.t
read ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored alignments. The stream stops after the first error.
val with_file : string ->
       f:(Header.t ->
          alignment Core.Std.Or_error.t Stream.t ->
          'a Core.Std.Or_error.t) ->
       'a Core.Std.Or_error.t
with_file fn ~f opens a BAM file for reading, applies f and closes the file after that, even if f raises an exception. Beware: the result of f should not lazily depend on the stream it receives as a second argument, since after the call to with_file the underlying channel is closed.
val write : Header.t ->
       alignment Stream.t ->
       Pervasives.out_channel -> unit Core.Std.Or_error.t
write h xs oc writes the header h and the alignments xs to oc.
end