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Module Biocaml_bam_alt.Alignment0 (.ml)

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.

module Alignment0:

sig

type t

val qname  : t -> string option

val flags  : t -> Biocaml_sam.Flags.t Core.Std.Or_error.t

val rname  : t ->
 Biocaml_bam_alt.Header.t -> string option Core.Std.Or_error.t

val pos  : t -> int option

val mapq  : t -> int option

val cigar  : t -> Biocaml_sam.cigar_op list Core.Std.Or_error.t

val rnext  : t ->
 Biocaml_bam_alt.Header.t -> Biocaml_sam.rnext option Core.Std.Or_error.t

val pnext  : t -> int option

val tlen  : t -> int option

val seq  : t -> string option

val qual  : t ->
 Biocaml_phred_score.t list Core.Std.Or_error.t

val optional_fields  : t ->
 Biocaml_sam.optional_field list Core.Std.Or_error.t

val decode  : t ->
 Biocaml_bam_alt.Header.t -> Biocaml_bam_alt.alignment Core.Std.Or_error.t

val encode  : Biocaml_bam_alt.alignment ->
 Biocaml_bam_alt.Header.t -> t Core.Std.Or_error.t

val t_of_sexp  : Sexplib.Sexp.t -> t

val sexp_of_t  : t -> Sexplib.Sexp.t

end