ailist.IntervalArray

class ailist.IntervalArray

IntervalArray stores a list of intervals

Attributes

ends	End values
is_closed	Whether object is still in memory
is_constructed	Whether IntervalArray is constructed or not
is_frozen	Whether object is immutable
range	Ranges(start, end) for each label
size	Number of intervals in IntervalArray
starts	Start values

Methods

add(start, end)	Add an interval to IntervalArray inplace
append(other_ail)	Add intervals from arrays to IntervalArray inplace
bin_nhits([bin_size, min_length, max_length])	Find number of intervals overlapping binned positions
close()	Close object and clear memory
construct([min_length])	Construct labeled_aiarray_t *Required to call intersect
copy()	Copy IntervalArray
coverage([min_length, max_length])	Calculate coverage for each position in IntervalArray range
create_bin(bin_range[, bin_size])
downsample(proportion[, return_intervals, ...])	Randomly downsample IntervalArray
filter([min_length, max_length])	Filter out intervals outside of a length range
filter_exact_match(other_aiarray)	Determine which intervals are present
freeze()	Make IntervalArray immutable
has_exact_match(other_aiarray)	Determine which intervals are present
has_hit(start, end)	Find interval indices overlapping given ranges
index_with_aiarray(other_aiarray)
intersect(start, end[, return_intervals, ...])	Find intervals overlapping given range
intersect_from_IntervalArray(ail_query[, ...])	Find interval indices overlapping given ranges
iter_intersect(query_laia[, ...])
iter_sorted()	Iterate over an IntervalArray in sorted way
length_dist()	Calculate length distribution of intervals
merge([gap])	Merge intervals within a gap
nhits(start, end[, min_length, max_length])	Find number of intervals overlapping given positions
nhits_from_IntervalArray(query_laia[, ...])	Find number of intervals overlapping
simulate()
sort()
sorted_index()
unfreeze()	Make IntervalArray mutable
validate_construction()
wps([protection, min_length, max_length])	Calculate Window Protection Score for each position in IntervalArray range