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cljam.util.region

Utility functions for manipulating chromosomal regions.

Utility functions for manipulating chromosomal regions.
raw docstring

complement-regionsclj

(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.

Returns a sequence of regions complement to in-regions.
in-regions must be sorted.
Returns a stateful transducer when no regions provided.
sourceraw docstring

divide-refsclj

(divide-refs refs step)

Divides refs into several chunks with maximum length 'step'. Returns a lazy sequence of map containing {:chr :start :end}.

Divides refs into several chunks with maximum length 'step'.
Returns a lazy sequence of map containing {:chr :start :end}.
sourceraw docstring

divide-regionclj

(divide-region start end step)

Divides a region [start end] into several chunks with maximum length 'step'. Returns a lazy sequence of vector.

Divides a region [start end] into several chunks with maximum length 'step'.
Returns a lazy sequence of vector.
sourceraw docstring

format-regionclj

(format-region {:keys [chr start end]})

Format a region map into a string.

Format a region map into a string.
sourceraw docstring

format-region-strictclj

(format-region-strict region-map)

Format a region map into a string strictly.

Format a region map into a string strictly.
sourceraw docstring

merge-regionsclj

(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.

Same as 'merge-regions-with' except for 'merge-two-regions' is
partially applied as merge-fn.
sourceraw docstring

merge-regions-withclj

(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.

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.
sourceraw docstring

overlapped-regions?clj

(overlapped-regions? x y)

Returns true if two regions are overlapped with each other.

Returns true if two regions are overlapped with each other.
sourceraw docstring

parse-regionclj

(parse-region region-str)

Parse a region string into a map.

Parse a region string into a map.
sourceraw docstring

parse-region-strictclj

(parse-region-strict region-str)

Parse a region string into a map strictly.

Parse a region string into a map strictly.
sourceraw docstring

subtract-regionclj

(subtract-region lhs-reg rhs-reg)

Subtract a region from another one. Returns a vector of regions.

Subtract a region from another one.
Returns a vector of regions.
sourceraw docstring

valid-region?clj

(valid-region? {:keys [chr start end]})

Checks if the given region map is a valid 1-based closed range.

Checks if the given region map is a valid 1-based closed range.
sourceraw docstring

valid-rname?clj

(valid-rname? rname)

Checks if the given rname conforms to the spec of sam.

Checks if the given rname conforms to the spec of sam.
sourceraw docstring

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