package biocaml

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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.

module Header : sig ... end

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

type alignment = Sam.alignment
module Alignment0 : sig ... end

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.

with_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.

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.

with_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.

Low-level access

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