Module Biocaml_bed (.ml)

module Biocaml_bed: sig .. end

BED data. A BED file is in the format shown below, where columns must be separted by a tab character.

    chrA   lo1   hi1
    chrA   lo2   hi2
    .      .     .
    .      .     .
    .      .     .
    chrB   lo1   hi1
    chrB   lo2   hi2
    .      .     .
    .      .     .
    .      .     .
   

The definition is that intervals are zero based and half-open. So by default the line "chrA lo hi" is parsed to the interval [lo + 1, hi] on chromosome chrA. Similarly, when printing, the default is to print [lo - 1, hi]. The optional argument increment_lo_hi allows changing this behavior for non-conformant files. In addition, the optional argument chr_map is a string -> string function that allows changing of the chromosome name to a specified format, and defaults to identity.

Some tools require that the set of intervals do not overlap within each chromosome. This is not enforced, but you can use any_overlap to verify this property when needed.

type item = string * int * int * Biocaml_table.Row.t 

The type of BED data stream items.

type parsing_spec = [ `enforce of Biocaml_table.Row.t_type | `strings ] 

The specification of how to parse the remaining columns.

module Error: sig .. end

val item_of_line : how:parsing_spec ->
       Biocaml_lines.item ->
       (item, [> Error.parsing ]) Core.Result.t

Basic parsing of a single line.

val item_to_line : item -> Biocaml_lines.item

Basic “printing” of one single item.

module Transform: sig .. end

val item_of_sexp : Sexplib.Sexp.t -> item

val sexp_of_item : item -> Sexplib.Sexp.t

The type of BED data stream items.

val parsing_spec_of_sexp : Sexplib.Sexp.t -> parsing_spec

val parsing_spec_of_sexp__ : Sexplib.Sexp.t -> parsing_spec

val sexp_of_parsing_spec : parsing_spec -> Sexplib.Sexp.t

The specification of how to parse the remaining columns.