[ gia closest ]
Background
Similar to intersect, closest
searches for the closest
feature in B
for each feature in A
.
The closest
feature is not necessarily non-overlapping and under certain
search constraints may not exist.
Note: Chromosomal Distance
There is no notion of interchromosomal distance, so if an interval is alone on an interval in
A
, then there will be no closest interval inB
.
Usage
See full arguments and options using:
gia closest --help
Default Behavior
(a) x----------y
(b) i-----j i-------j
=========================================
i-----j
By default closest
will return the single closest, potentially overlapping, feature in B
for each interval in A
.
Ties will be given to the left-most interval with the closest start coordinate to the query.
gia closest -a <input.bed> -b <input.bed>
Closest Upstream
(a) x----------y
(b) i-----j i-------j
=========================================
i-----j
You can explicitly exclude all downstream intervals from the search, regardless of their distance, with the upstream flag.
gia closest -a <input.bed> -b <input.bed> -u
Closest Downstream
(a) x----------y
(b) i-----j i-------j
=========================================
i-------j
You can explicitly exclude all upstream intervals from the search, regardless of their distance, with the downstream flag.
gia closest -a <input.bed> -b <input.bed> -d