Commit 814673f8 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: e-values, -e/-E

parent e6ffb915
...@@ -382,6 +382,9 @@ the clone sequence and the V(D)J germline genes. The default values should work. ...@@ -382,6 +382,9 @@ the clone sequence and the V(D)J germline genes. The default values should work.
(meaning that V and J could overlap 10 bp). This is the default for VJ recombinations (meaning that V and J could overlap 10 bp). This is the default for VJ recombinations
(except when using a =germlines.data= file). (except when using a =germlines.data= file).
The e-value set by =-e= is also applied to the V/J designation.
The =-E= option further sets the e-value for the detection of D segments.
** Further clustering (experimental) ** Further clustering (experimental)
The following options are experimental and have no consequences on the =.vdj.fa= file, The following options are experimental and have no consequences on the =.vdj.fa= file,
...@@ -394,7 +397,7 @@ being +1 for a match and -4 for a mismatch). However, more distant reads can als ...@@ -394,7 +397,7 @@ being +1 for a match and -4 for a mismatch). However, more distant reads can als
be clustered when there are more than 10 reads within the distance threshold. be clustered when there are more than 10 reads within the distance threshold.
This behaviour can be controlled with the =-N= option. This behaviour can be controlled with the =-N= option.
The =-E= option allows to specify a file for manually clustering two windows The =-== option allows to specify a file for manually clustering two windows
considered as similar. Such a file may be automatically produced by vidjil considered as similar. Such a file may be automatically produced by vidjil
(=out/edges=), depending on the option provided. Only the two first columns (=out/edges=), depending on the option provided. Only the two first columns
(separed by one space) are important to vidjil, they only consist of the (separed by one space) are important to vidjil, they only consist of the
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