package biocaml
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doc/biocaml.unix/Biocaml_unix/Bam/index.html
Module Biocaml_unix.Bam
Read and write BAM format.
The implementation does its best to comply with the official specification.
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_kernel.In_channel.t ->
(Header.t * Alignment0.t Core_kernel.Or_error.t Stream.t)
Core_kernel.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_kernel.Or_error.t Stream.t ->
'a Core_kernel.Or_error.t) ->
'a Core_kernel.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 Stream.t ->
Core_kernel.Out_channel.t ->
unitwrite0 h xs oc writes the header h and (partially parsed) alignments xs to oc.
val read :
Core_kernel.In_channel.t ->
(Header.t * alignment Core_kernel.Or_error.t Stream.t) Core_kernel.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_kernel.Or_error.t Stream.t ->
'a Core_kernel.Or_error.t) ->
'a Core_kernel.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 Stream.t ->
Core_kernel.Out_channel.t ->
unit Core_kernel.Or_error.twrite h xs oc writes the header h and the alignments xs to oc.
Low-level access
val read_header : Bgzf.in_channel -> Header.t Core_kernel.Or_error.tval read_alignment :
Bgzf.in_channel ->
Alignment0.t Core_kernel.Or_error.t optionval read_alignment_stream :
Bgzf.in_channel ->
Alignment0.t Core_kernel.Or_error.t Stream.t