Commit 0644f019 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Marc Duez
Browse files

vidjil.cpp: output 'out/segmented.vdj.fa' only when the new option '-U' is set.

A very long time ago, 'out/segmented.vdj.fa' was considered to be
the main output of Vidjil, giving the (heuristic) segmentation of
each read. However, when many reads are segmented, writing this file
to the disk can slow the software (until 25%)... and this file
was used only to debug. By default, this file is now not produced.

The main output, with a summary of windows and representative, is in
'out/windows.fa', 'out/seq/clone.fa-' and now 'out/vidjil.data'.
parent 29f414ce
......@@ -195,7 +195,8 @@ void usage(char *progname)
<< endl
<< "Debug" << endl
<< " -u output unsegmented sequences (default: " << UNSEGMENTED_FILENAME << ")" << endl
<< " -U output segmented (" << SEGMENTED_FILENAME << ") sequences" << endl
<< " -u output unsegmented (" << UNSEGMENTED_FILENAME << ") sequences" << endl
<< " and display detailed k-mer affectation both on segmented and on unsegmented sequences" << endl
<< "Output" << endl
<< " -o <dir> output directory (default: " << OUT_DIR << ")" << endl
......@@ -270,7 +271,7 @@ int main (int argc, char **argv)
bool output_sequences_by_cluster = false;
bool detailed_cluster_analysis = true ;
bool very_detailed_cluster_analysis = false ;
bool output_segmented = true;
bool output_segmented = false;
bool output_unsegmented = false;
string forced_edges = "" ;
......@@ -287,7 +288,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "AhaG:V:D:J:k:r:R:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:u")) != EOF)
while ((c = getopt(argc, argv, "AhaG:V:D:J:k:r:R:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:Lx%:Z:z:uU")) != EOF)
switch (c)
{
......@@ -451,6 +452,9 @@ int main (int argc, char **argv)
case 'u':
output_unsegmented = true;
break;
case 'U':
output_segmented = true;
break;
}
// If there was no -w option, then w is either DEFAULT_W or DEFAULT_W_D
......
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