package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

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

Module `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.

type t

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

val t_of_sexp : Sexplib0.Sexp.t -> t

val sexp_of_t : t -> Sexplib0.Sexp.t

val qname : t -> string option

val flags : t -> Sam.Flags.t Core_kernel.Or_error.t

val rname : t -> Header.t -> string option Core_kernel.Or_error.t

val pos : t -> int option

Positions are 0-based, -1 if undefined

val mapq : t -> int option

val cigar : t -> Sam.cigar_op list Core_kernel.Or_error.t

val rnext : t -> Header.t -> Sam.rnext option Core_kernel.Or_error.t

val pnext : t -> int option

val tlen : t -> int option

val seq : t -> string option

val qual : t -> Phred_score.t list Core_kernel.Or_error.t

val optional_fields : t -> Sam.optional_field list Core_kernel.Or_error.t

val decode : t -> Header.t -> alignment Core_kernel.Or_error.t

val encode : alignment -> Header.t -> t Core_kernel.Or_error.t