package biocaml

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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.

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.

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.

write0 h xs oc writes the header h and (partially parsed) alignments xs to oc.

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.

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

Low-level access

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