Commit bf2f96fe authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: -t 100 is now the default

Partially revert de92e254
parent fbbb9b36
......@@ -116,7 +116,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_CLUSTER_COST Cluster
#define DEFAULT_SEGMENT_COST VDJ
#define DEFAULT_TRIM 0
#define DEFAULT_TRIM 100
// error
#define ERROR_STRING "[error] "
......
......@@ -161,7 +161,7 @@ Window prediction
-M <int> maximal admissible delta between last V and first J k-mer (default: 20) (default with -D: 80)
-w <int> w-mer size used for the length of the extracted window (default: 50)
-e <float> maximal e-value for determining if a segmentation can be trusted (default: 'all', no limit)
-t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: 0) (0: no trim)
-t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: 100) (0: no trim)
#+END_EXAMPLE
The =-s=, =-k=, =-m= and =-M= options are the options of the seed-based heuristic. A detailed
......@@ -209,8 +209,7 @@ The threshold can be disabled with =-e all=.
The =-t= option sets the maximal number of nucleotides that will be indexed in
V genes (the 3' end) or in J genes (the 5' end). This reduces the load of the
indexes, giving more precise window estimation and e-value computation.
This option is currently not set, it will be set by default in a next release.
Using =-t 100= is generally safe.
The default is =-t 100=.
** Threshold on clone output
......
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