Used in: gor only

SEGWHERE

The SEGWHERE command turns a stream of annotations into a stream of non-overlapping segments. The output is Chrom, bpStart, bpStop. Use -minseg size to set the minimum segment size required to be considered a segment. Using the -sh``option will start the segment halfway from the previous false condition. If the first available row meets the condition then the segment starts at the row position. Using the ``-eh option will end the segment halfway from the previous true condition. If the last available row meets the condition then the segment ends at the row position.

Usage

gor ... | segwhere -minseg 1000 -sh -eh ref != 'T'

Options

-minseg size	Minimum segment size required to be considered a segment. Default is unlimited
-sh	Segment starts halfway from previous false condition. If first available row meets the condition then the segment starts at row position.
-eh	Segment ends halfway from previous true condition. If last available row meets the condition then the segment ends at row position.