Commit 19103813 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: option '-d' for multiple D detection

VDDJ segmentation is still somewhat experimental.
Moreover, it will have someday some consequence on the json output, that are not always desirable.
We prefer thus to keep this optional.
parent 1967b490
......@@ -167,6 +167,7 @@ void usage(char *progname, bool advanced)
<< endl
<< "Locus/recombinations" << endl
<< " -d try to detect several D (experimental)" << endl
<< " -i try to detect incomplete/unusual recombinations (locus with '+', must be used with -g)" << endl
<< " -2 try to detect unexpected recombinations (must be used with -g)" << endl
<< endl ;
......@@ -356,6 +357,8 @@ int main (int argc, char **argv)
bool output_affects = false;
bool keep_unsegmented_as_clone = false;
bool several_D = false;
bool multi_germline = false;
bool multi_germline_incomplete = false;
bool multi_germline_mark = false;
......@@ -384,7 +387,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHaiI124g:G:V:D:J:k:r:vw:e:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:G:V:D:J:k:r:vw:e:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:")) != EOF)
switch (c)
{
......@@ -460,6 +463,10 @@ int main (int argc, char **argv)
germline_system = "multi" ;
break;
case 'd':
several_D = true;
break;
case 'i':
multi_germline_incomplete = true;
break;
......@@ -1355,7 +1362,7 @@ int main (int argc, char **argv)
FineSegmenter seg(representative, segmented_germline, segment_cost);
if (segmented_germline->seg_method == SEG_METHOD_543)
seg.FineSegmentD(segmented_germline);
seg.FineSegmentD(segmented_germline, several_D);
if (detect_CDR3)
seg.findCDR3();
......@@ -1571,7 +1578,7 @@ int main (int argc, char **argv)
if (s.isSegmented())
{
if (germline->seg_method == SEG_METHOD_543)
s.FineSegmentD(germline);
s.FineSegmentD(germline, several_D);
if (detect_CDR3)
s.findCDR3();
......
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