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

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