cljam.util.region
Utility functions for manipulating chromosomal regions.
complement-regions
(complement-regions base-region)(complement-regions base-region in-regions)
Returns a sequence of regions complement to in-regions.
in-regions must be sorted.
Returns a stateful transducer when no regions provided.
divide-refs
(divide-refs refs step)
Divides refs into several chunks with maximum length 'step'.
Returns a lazy sequence of map containing {:chr :start :end}.divide-region
(divide-region start end step)
Divides a region [start end] into several chunks with maximum length 'step'.
Returns a lazy sequence of vector.
merge-regions
(merge-regions)(merge-regions max-gap)(merge-regions max-gap regions)
Same as 'merge-regions-with' except for 'merge-two-regions' is
partially applied as merge-fn.
merge-regions-with
(merge-regions-with merge-fn)(merge-regions-with merge-fn max-gap)(merge-regions-with merge-fn max-gap regs)
Returns a lazy sequence of merged regions. Input regions must be sorted.
Neighboring regions apart less than or equal to 'max-gap' will be merged
with 'merge-fn'. Returns a stateful transducer when no input 'regions' is
provided.
overlapped-regions?
(overlapped-regions? {x-start :start, x-end :end, x-chr :chr} {y-start :start, y-end :end, y-chr :chr})
Returns true if two regions are overlapped with each other.
parse-region
(parse-region region-str)
Parse a region string into a map.
parse-region-strict
(parse-region-strict region-str)
Parse a region string into a map strictly.
subtract-region
(subtract-region lhs-reg {rhs-reg-start :start, rhs-reg-end :end, rhs-reg-chr :chr})
Subtract a region from another one.
Returns a vector of regions.
valid-region?
(valid-region? {:keys [chr start end]})
Checks if the given region map is a valid 1-based closed range.
valid-rname?
(valid-rname? rname)
Checks if the given rname conforms to the spec of sam.