cljam.util.whole-genome — cljam 0.8.3

Utilities for conversions between chromosomal positions and whole-genome positions.

->chr-and-pos clj

(->chr-and-pos offset->ref wg-pos)

Transforms a whole-genome position to a vector of a chromosome name and a position in the chromosome.

->regions clj

(->regions offset->ref start end)

Transforms a region in whole-genome coordinate into a sequence of chromosomal regions.

->whole-genome-coord clj

(->whole-genome-coord chr->offset chr pos)

Transforms a position in a chromosome into a whole-genome position.

chr-to-whole-genome-index clj

(chr-to-whole-genome-index refs)

Creates a map of [chromosome-name offset&length] from refs.

whole-genome-to-chr-index clj

(whole-genome-to-chr-index refs)

Creates a sorted-map of [offset chromosome-name&length] from refs.