package biocaml

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package biocaml
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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.

type t = private {
  1. lo : int;
  2. hi : int;
}

Type of a range.

include sig ... end
val compare : t -> t -> int
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
val make : int -> int -> t Core_kernel.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 -> [ `Joint of t | `Disjoint of t * 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 Math.find_regions.

val make_random : t -> t

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.

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