Read and write BAM format.
The implementation does its best to comply with the official specification.
Note: this module was adapted from biocaml 0.8
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 Sam module.
module Header : sig ... endBAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.
type alignment = Sam.alignmentmodule Alignment0 : sig ... endRepresentation 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.
val read0 :
Core.In_channel.t ->
(Header.t * Alignment0.t Core.Or_error.t Stdlib.Seq.t) Core.Or_error.tread0 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.Or_error.t Stdlib.Seq.t ->
'a Core.Or_error.t) ->
'a Core.Or_error.twith_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 Stdlib.Seq.t ->
Core.Out_channel.t ->
unitwrite0 h xs oc writes the header h and (partially parsed) alignments xs to oc.
val read :
Core.In_channel.t ->
(Header.t * alignment Core.Or_error.t Stdlib.Seq.t) Core.Or_error.tread 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.Or_error.t Stdlib.Seq.t -> 'a Core.Or_error.t) ->
'a Core.Or_error.twith_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 Stdlib.Seq.t ->
Core.Out_channel.t ->
unit Core.Or_error.twrite h xs oc writes the header h and the alignments xs to oc.
val read_header : Bgzf.in_channel -> Header.t Core.Or_error.tval read_alignment : Bgzf.in_channel -> Alignment0.t Core.Or_error.t optionval read_alignment_stream :
Bgzf.in_channel ->
Alignment0.t Core.Or_error.t Stdlib.Seq.t