package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

doc/biocaml.unix/Biocaml_unix/Bam/Alignment0/index.html

Module `Bam.Alignment0`Source

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.

Sourcetype t

include Sexplib0.Sexpable.S with type t := t

Sourceval t_of_sexp : Sexplib0.Sexp.t -> t

Sourceval sexp_of_t : t -> Sexplib0.Sexp.t

Sourceval qname : t -> string option

Sourceval flags : t -> Sam.Flags.t Core.Or_error.t

Sourceval ref_id : t -> int option

Sourceval rname : t -> Header.t -> string option Core.Or_error.t

Sourceval pos : t -> int option

Positions are 0-based, -1 if undefined

Sourceval mapq : t -> int option

Sourceval cigar : t -> Sam.cigar_op list Core.Or_error.t

Sourceval rnext : t -> Header.t -> Sam.rnext option Core.Or_error.t

Sourceval pnext : t -> int option

Sourceval tlen : t -> int option

Sourceval seq : t -> string option

Sourceval qual : t -> Phred_score.t list Core.Or_error.t

Sourceval optional_fields : t -> Sam.optional_field list Core.Or_error.t

Sourceval decode : t -> Header.t -> alignment Core.Or_error.t

Sourceval encode : alignment -> Header.t -> t Core.Or_error.t