API Reference

Both strand ('.')

Unknown strand ('?')

Negative strand ('-')

Positive strand ('+')

A genomic interval specifies interval with some associated metadata

Return true if interval a overlaps interval b, with no consideration to strand

leftposition(i::Interval)

Return the leftmost position of i.

rightposition(i::Interval)

Return the rightmost position of i.

coverage(intervals)

Compute the coverage of a collection of intervals and return an IntervalCollection that contains run-length encoded coverage data.

For example, given intervals like:

[------]     [------------]
   [---------------]

This function would return a new set of disjoint intervals with annotated coverage like:

[1][-2-][-1-][--2--][--1--]

eachoverlap(intervals_a, intervals_b, [seqname_isless=Base.isless])

Create an iterator of overlapping intervals between intervals_a and intervals_b.

This function assumes elements of intervals_a and intervals_b are sorted by its sequence name and left position. If the element type is not a subtype of GenomicFeatures.Interval, elements are converted to Interval objects.

The third optional argument is a function that defines the order of sequence names. The default function is Base.isless, which is the lexicographical order.

Find a the first interval with matching start and end points.

Returns that interval, or 'nothing' if no interval was found.

Check if two intervals are well ordered.

Intervals are considered well ordered if a.seqname <= b.seqnamend and a.first <= b.first.

Return true if interval a entirely precedes b.