package biocaml

You can search for identifiers within the package.

in-package search v0.2.0

The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.11.1.tar.gz

md5=e292efa2f61fec33dad63ec897106f59

sha512=35519bf3b1e67a9191ef9bb74eba0dae941e0d05bad89076a36f507dc5c2d105a03c1c917d5a3f7ed9d1da4acbf3199582f78c308aa2a5a22c21f743945c852b

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 Ppx_sexp_conv_lib.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_kernel.Or_error.t

Sourceval rname : t -> Header.t -> string option Core_kernel.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_kernel.Or_error.t

Sourceval rnext : t -> Header.t -> Sam.rnext option Core_kernel.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_kernel.Or_error.t

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

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

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