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Module Biocaml_range (.ml)

Ranges of contiguous integers (integer intervals). A range is a contiguous sequence of integers from a lower bound to an upper bound. For example, [2, 10] is the set of integers from 2 through 10, inclusive of 2 and 10.

module Biocaml_range:
sig
type t = private {
   lo : int;
   hi : int;
}
Type of a range.
val make : int -> int -> t Core.Std.Or_error.t
make lo hi returns the range {lo; hi}. Return Error if lo > hi.
val make_unsafe : int -> int -> t
val size : t -> int
size v returns the number of integers in v, i.e. v.hi - v.lo + 1.
val member : t -> int -> bool
member t k returns true if t contains k.
val to_string : t -> string
String representation of an range, intended only for human legibility.
val to_list : t -> int list
to_list v returns the set of integers contained in v, in ascending order.
val overlap : t -> t -> int
overlap u v returns amount of overlap between two ranges. A positive value indicates number of integers common to u and v. A negative value indicates the number of integers in between non-overlapping ranges. A zero value means the ranges are exactly adjacent to each other. The relation is symmetric.
val gap : t -> t -> int
gap u v returns the size of the gap between u and v. It is equivalent to the negative of overlap.

Set Operations

val union : t ->
       t ->
       [ `Disjoint of t * t | `Joint of t ]
union u v returns the range(s) representing the union of u and v. If u and v overlap, their union can be represented as a single range. If not, their union is a disjoint combination of two ranges.
val intersect : t -> t -> t option
intersect u v returns the range representing the intersection of u and v. Return None if intersection is empty.

Positional Range
Positional means an range is viewed as coming either before or after another.
val before : t -> t -> bool
before u v is true if strict_before u v || equal u v.
val after : t -> t -> bool
after u v is equivalent to before v u.
val strict_before : t -> t -> bool
strict_before u v is true if u.lo < v.lo && u.hi < v.hi.
val strict_after : t -> t -> bool
strict_after u v is equivalent to strict_before v u.
val compare_positional : t -> t -> int option
compare_positional u v returns -1 if u is strictly before v, 0 if u is equal to v, +1 if u is strictly after v, and returns None otherwise.

Containment Range
Containment means a range is viewed as being inside, or a subset of, another.
val subset : t -> t -> bool
subset u v is true if u is a subset of v.
val superset : t -> t -> bool
superset u v is true if u is a superset of v.
val strict_subset : t -> t -> bool
strict_subset u v is true if u is a strict subset of v.
val strict_superset : t -> t -> bool
strict_superset u v is true if u is a strict superset of v.
val compare_containment : t -> t -> int option
compare_containment u v returns -1 if u is a strict subset of v, 0 if u is equal to v, +1 if u is a strict superset of v, and returns None otherwise.

Range Lists

val any_overlap : t list -> bool
Return true if any pair of given ranges overlap each other.
val all_positional : t list -> bool
Return true if all pairs of given ranges are positionally comparable.
val max_gap_of_positional : t list -> int
Return maximum gap between adjacent pairs of given ranges. Raise Failure if any pairs of given ranges not positionally comparable, or if given less than two ranges.

More Specialized Operations

val find_min_range : ?init_direction:string ->
       t -> (t -> bool) -> int -> t option
find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred. Successively larger ranges are created starting from [i, i] and the first one to satisfy pred is returned. None is returned if the given range v itself is reached and pred still fails. Raise Failure if i not within v.

The first range tried is [i, i], by default the second is [i, i+1], the third [i-1, i+1], the fourth [i-1, i+2], and so on. The optional init_direction must be either "fwd" or "rev". If "fwd", which is the default, the range size is initially increased in the forward direction. If "rev", the second range tried will be [i-1, i]. If the range boundary is reached on either side, the size continues to be increased by incrementing on the opposing side.

val expand_assoc_list : (t * 'a) list -> (int * 'a list) list
exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat. The set of integers considered is the union of all in given dat.
val find_regions : ?max_gap:int ->
       ('a -> bool) -> (t * 'a) list -> t list
TO DO: fill in this documentation. For now see Biocaml_math.find_regions.
val make_random : t -> t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
val compare : t -> t -> int

make lo hi returns the range {lo; hi}. Return Error if lo > hi.

size v returns the number of integers in v, i.e. v.hi - v.lo + 1.

member t k returns true if t contains k.

String representation of an range, intended only for human legibility.

to_list v returns the set of integers contained in v, in ascending order.

overlap u v returns amount of overlap between two ranges. A positive value indicates number of integers common to u and v. A negative value indicates the number of integers in between non-overlapping ranges. A zero value means the ranges are exactly adjacent to each other. The relation is symmetric.

gap u v returns the size of the gap between u and v. It is equivalent to the negative of overlap.

Set Operations


union u v returns the range(s) representing the union of u and v. If u and v overlap, their union can be represented as a single range. If not, their union is a disjoint combination of two ranges.

intersect u v returns the range representing the intersection of u and v. Return None if intersection is empty.

Positional Range
Positional means an range is viewed as coming either before or after another.

before u v is true if strict_before u v || equal u v.

after u v is equivalent to before v u.

strict_before u v is true if u.lo < v.lo && u.hi < v.hi.

strict_after u v is equivalent to strict_before v u.

compare_positional u v returns -1 if u is strictly before v, 0 if u is equal to v, +1 if u is strictly after v, and returns None otherwise.

Containment Range
Containment means a range is viewed as being inside, or a subset of, another.

subset u v is true if u is a subset of v.

superset u v is true if u is a superset of v.

strict_subset u v is true if u is a strict subset of v.

strict_superset u v is true if u is a strict superset of v.

compare_containment u v returns -1 if u is a strict subset of v, 0 if u is equal to v, +1 if u is a strict superset of v, and returns None otherwise.

Range Lists


Return true if any pair of given ranges overlap each other.

Return true if all pairs of given ranges are positionally comparable.

Return maximum gap between adjacent pairs of given ranges. Raise Failure if any pairs of given ranges not positionally comparable, or if given less than two ranges.

More Specialized Operations


find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred. Successively larger ranges are created starting from [i, i] and the first one to satisfy pred is returned. None is returned if the given range v itself is reached and pred still fails. Raise Failure if i not within v.

The first range tried is [i, i], by default the second is [i, i+1], the third [i-1, i+1], the fourth [i-1, i+2], and so on. The optional init_direction must be either "fwd" or "rev". If "fwd", which is the default, the range size is initially increased in the forward direction. If "rev", the second range tried will be [i-1, i]. If the range boundary is reached on either side, the size continues to be increased by incrementing on the opposing side.


exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat. The set of integers considered is the union of all in given dat.

TO DO: fill in this documentation. For now see Biocaml_math.find_regions.

make_random t returns a random range that is a subset of t. May raise Failure if given range bounds exceed largest value handled by Random module.
end