cljam.io.util.bin — cljam 0.8.4

bin-beg clj

(bin-beg bin min-shift depth)

Returns a beginning position of the given bin. 1-based.

bin-level clj

(bin-level bin)

Returns a level that the given bin belongs to.

bin-width-of-level clj

(bin-width-of-level level min-shift depth)

Returns a width shared by bins of the same given level.

first-bin-of-level clj

(first-bin-of-level level)

Returns a left-most bin number of the given level.

get-spans clj

(get-spans index-data ref-idx beg end)

Calculates span information for random access from index data such as tabix.

IBinningIndex clj protocol

get-chr-names clj

(get-chr-names this)

get-chunks clj

(get-chunks this ref-idx bins)

get-depth clj

(get-depth this)

get-min-offset clj

(get-min-offset this ref-idx beg)

get-min-shift clj

(get-min-shift this)

leading-bins-at-level clj

(leading-bins-at-level pos level min-shift depth)

Returns the distance between the bin corresponding to pos and the first one at the same level.

max-bin clj

(max-bin depth)

Returns a maximum bin number of a binning index with the given depth.

max-pos clj

(max-pos min-shift depth)

Returns a maximum position of a binning index. The value is identical to the width of bin 0.

parent-bin clj

(parent-bin bin)

Returns the bin number of the parent bin.

pos->lidx-offset clj

(pos->lidx-offset pos linear-index-shift)

Returns an offset of a linear index that the given pos belongs to.

reg->bin clj

(reg->bin beg end min-shift depth)

Calculates the smallest bin containing the given region [beg, end].

reg->bins clj

(reg->bins beg end min-shift depth)

Returns all overlapping bins for the specified region [beg, end] as a vector.