Commit 47a7c984 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: new option '-E', D e-value threshold

parent dac673df
......@@ -194,7 +194,7 @@ void usage(char *progname, bool advanced)
<< " (using -k option is equivalent to set with -s a contiguous seed with only '#' characters)" << endl
#endif
<< " -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
<< " -e <float> maximal e-value for determining if a V-J 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 << ") (0: no trim)" << endl
<< endl
......@@ -221,6 +221,7 @@ void usage(char *progname, bool advanced)
cerr << "Fine segmentation options (second pass)" << endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (default "<<VDJ<<" )"<< endl
<< " -m <int> minimal admissible delta between the end of the V and the start of the J (default: " << DEFAULT_DELTA_MIN << ") (default with -D: " << DEFAULT_DELTA_MIN_D << ")" << endl
<< " -E <float> maximal e-value for determining if a D segment can be trusted (default: " << THRESHOLD_NB_EXPECTED_D << ")" << endl
<< endl ;
cerr << "Clone analysis (second pass)" << endl
......@@ -386,6 +387,7 @@ int main (int argc, char **argv)
int options_s_k = 0 ;
double expected_value = THRESHOLD_NB_EXPECTED;
double expected_value_D = THRESHOLD_NB_EXPECTED_D;
//json which contains the Levenshtein distances
json jsonLevenshtein;
......@@ -394,7 +396,7 @@ int main (int argc, char **argv)
//$$ options: getopt
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:uUK3=:t:#:")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHadiI124g:G:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3=:t:#:")) != EOF)
switch (c)
{
......@@ -543,6 +545,10 @@ int main (int argc, char **argv)
expected_value = atof_NO_LIMIT(optarg);
break;
case 'E':
expected_value_D = atof_NO_LIMIT(optarg);
break;
// Output
case 'o':
......@@ -1380,7 +1386,7 @@ 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, several_D);
seg.FineSegmentD(segmented_germline, several_D, expected_value_D);
if (detect_CDR3)
seg.findCDR3();
......@@ -1597,7 +1603,7 @@ int main (int argc, char **argv)
if (s.isSegmented())
{
if (germline->seg_method == SEG_METHOD_543)
s.FineSegmentD(germline, several_D);
s.FineSegmentD(germline, several_D, expected_value_D);
if (detect_CDR3)
s.findCDR3();
......
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