package biocaml
Install
Dune Dependency
Authors
Maintainers
Sources
md5=e292efa2f61fec33dad63ec897106f59
sha512=35519bf3b1e67a9191ef9bb74eba0dae941e0d05bad89076a36f507dc5c2d105a03c1c917d5a3f7ed9d1da4acbf3199582f78c308aa2a5a22c21f743945c852b
doc/biocaml.ez/Biocaml_ez/Bam/index.html
Module Biocaml_ez.BamSource
include module type of struct include Biocaml_unix.Bam end
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.
BAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.
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.
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.
write0 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.
Low-level access
val 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.t