include module type of struct include Biocaml_unix.Bam endA 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 = Biocaml_unix.Bam.HeaderBAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.
type alignment = Biocaml_unix.Sam.alignmentmodule Alignment0 = Biocaml_unix.Bam.Alignment0Representation 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 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 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.
val read_header :
Biocaml_unix.Bgzf.in_channel ->
Header.t Core_kernel.Or_error.tval read_alignment :
Biocaml_unix.Bgzf.in_channel ->
Alignment0.t Core_kernel.Or_error.t optionval read_alignment_stream :
Biocaml_unix.Bgzf.in_channel ->
Alignment0.t Core_kernel.Or_error.t Stream.tval with_file :
string ->
f:(Header.t -> alignment CFStream.Stream.t -> 'a) ->
'aval with_file0 :
string ->
f:(Header.t -> Alignment0.t CFStream.Stream.t -> 'a) ->
'a