package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

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biocaml@googlegroups.com

Sources

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

doc/biocaml.ez/Biocaml_ez/Bam/index.html

Module `Biocaml_ez.Bam`

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.

module Header = Biocaml_unix.Bam.Header

BAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.

type alignment = Biocaml_unix.Sam.alignment

module Alignment0 = Biocaml_unix.Bam.Alignment0

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.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 write0 : 
  Header.t ->
  Alignment0.t Stream.t ->
  Core_kernel.Out_channel.t ->
  unit

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.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 write : 
  Header.t ->
  alignment Stream.t ->
  Core_kernel.Out_channel.t ->
  unit Core_kernel.Or_error.t

write h xs oc writes the header h and the alignments xs to oc.

Low-level access

val read_header : 
  Biocaml_unix.Bgzf.in_channel ->
  Header.t Core_kernel.Or_error.t

val read_alignment : 
  Biocaml_unix.Bgzf.in_channel ->
  Alignment0.t Core_kernel.Or_error.t option

val read_alignment_stream : 
  Biocaml_unix.Bgzf.in_channel ->
  Alignment0.t Core_kernel.Or_error.t Stream.t

val with_file : 
  string ->
  f:(Header.t -> alignment CFStream.Stream.t -> 'a) ->
  'a

val with_file0 : 
  string ->
  f:(Header.t -> Alignment0.t CFStream.Stream.t -> 'a) ->
  'a