Commit 6b58dc54 authored by Marc Duez's avatar Marc Duez

Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil into rework_data

parents ee6b28b7 f59bcd13
!LAUNCH: (cd ../.. ; ./vidjil -c germlines data/Stanford_S22.fasta)
$ number of reads and kmers
1:13153 reads, 3020179 kmers
$ k-mers, IGHV
1:13148 .* 1832628 .*IGHV
$ k-mers, IGHJ
1:5 .* 407486 .*IGHJ
$ k-mers, ambiguous
1:98749 .*\?
$ k-mers, unknown
1:618185 .*_
!LAUNCH: ../../vidjil -h 2> out-v ; cat out-v
$ License
1:Vidjil is free software
$ Check default filtering options
1:minimal number of reads supporting a clone .*: 10
1:minimal percentage of reads supporting a clone .*: 0
1:maximal number of clones computed with a representative .*: 100
1:maximal number of clones to be segmented .*: 20
!LAUNCH: ../../vidjil -A
$ Warning, -A
1:WARNING
$ Link to documentation
1:algo.org
!LAUNCH: ../../vidjil -z 200
$ Warning, -z
1:WARNING
$ Link to documentation
1:algo.org
......@@ -741,7 +741,7 @@ int main (int argc, char **argv)
CountKmerAffectAnalyser<KmerAffect> ckaa(*index, seq);
ckaa.setAllowedOverlap(k-1);
stats_max[ckaa.max(forbidden).affect.c]++ ;
stats_max[affect_char(ckaa.max(forbidden).affect)]++ ;
}
......@@ -749,7 +749,10 @@ int main (int argc, char **argv)
// Display statistics
cout << " <== " << nb_reads << " reads" << endl ;
cout << " <== "
<< nb_reads << " reads, "
<< total_length << " kmers"
<< endl ;
cout << "\t" << " max" << "\t\t" << " kmers" << "\n" ;
for (list< pair <KmerAffect, string> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
......@@ -1293,6 +1296,8 @@ int main (int argc, char **argv)
delete json;
delete json_samples;
delete json_reads;
delete json_reads_germlineList;
delete multigermline ;
delete windowsStorage;
......
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