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.

---

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