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

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

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_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