Commit 6fd2fe69 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/ update help on e-value

parent f18ca797
......@@ -180,12 +180,12 @@ few more reads, but may in some rare cases falsely cluster reads from
different clones. Setting =-w= to lower values is not recommended.
The =-e= option sets the maximal e-value accepted for segmenting a sequence.
If a segmentation has a higher e-value, it will not be segmented.
It is an upper bound on the number of exepcted windows found by chance by the seed-based heuristic.
The e-value computation takes into account both the number of reads in the
input sequence and the number of locus searched for.
The default value is 'all', but the recommended value is to use something
like 1, 1e-2 or 1.
Further help on this point will come in next releases.
The default value is 1.0, but values such as 1000, 1e-3 or even less can be used
to have a more or less permissive segmentation.
The threshold can be disabled with =-e all=.
** Threshold on clone output
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