package biocaml
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sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d
sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6
doc/biocaml.unix/Biocaml_unix/Bam/index.html
Module Biocaml_unix.BamSource
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.
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.In_channel.t ->
(Header.t * Alignment0.t Core.Or_error.t Stream.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 Stream.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.
write0 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 Stream.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 Stream.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.
write h xs oc writes the header h and the alignments xs to oc.