Module Biocaml_bed

module Biocaml_bed: sig .. end

    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.

val enum_input : Batteries.IO.input -> (string * int * int) Batteries.Enum.t

val sqlite_db_of_enum : ?db:string ->
       ?table:string -> (string * int * int) Batteries.Enum.t -> Sqlite3.db