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.
typeitem =
string * int * int * Biocaml_table.Row.t
typeparsing_spec =
[ `enforce of Biocaml_table.Row.t_type | `strings ]
module Error:sig
..end
val item_of_line : how:parsing_spec ->
Biocaml_lines.item ->
(item, [> Error.parsing ]) Core.Result.t
val item_to_line : item -> Biocaml_lines.item
item
.module Transform:sig
..end
val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t
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
with sexp
)item
.Biocaml_transform.t
-based parser, while providing the
format of the additional columns (default `strings
).Biocaml_transform.t
which “prints” BED data
(reminder: includes ends-of-line).