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Commit de92e254 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil: -t option is unset by default

It will be default in a next release.
parent c6878803
......@@ -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 100
#define DEFAULT_TRIM 0
// error
#define ERROR_STRING "[error] "
......@@ -182,7 +182,7 @@ void usage(char *progname, bool advanced)
<< " -M <int> maximal admissible delta between last V and first J k-mer (default: " << DEFAULT_DELTA_MAX << ") (default with -D: " << DEFAULT_DELTA_MAX_D << ")" << endl
<< " -w <int> w-mer size used for the length of the extracted window (default: " << DEFAULT_W << ")" << endl
<< " -e <float> maximal e-value for determining if a segmentation can be trusted (default: " << THRESHOLD_NB_EXPECTED << ")" << endl
<< " -t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: " << DEFAULT_TRIM << ")" << endl
<< " -t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: " << DEFAULT_TRIM << ") (0: no trim)" << endl
<< endl
<< "Labeled windows (these windows will be kept even if -r/-% thresholds are not reached)" << endl
......
......@@ -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: 100)
-t <int> trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (default: 0) (0: no trim)
#+END_EXAMPLE
The =-s=, =-k=, =-m= and =-M= options are the options of the seed-based heuristic. A detailed
......@@ -191,9 +191,11 @@ to have a more or less permissive segmentation.
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). By default only 100nt will be
kept. This should be largely sufficient for the huge majority of
applications.
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.
** Threshold on clone output
The following options control how many clones are output and analyzed.
......
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