Commit b5fce172 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove 'delta_min', including '-m' option

'-m' was not very clear (#1673) because... 'delta_min' was never used.
See #1674.
parent 4d6567b2
......@@ -218,7 +218,6 @@ void usage(char *progname, bool advanced)
if (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 ;
......@@ -355,11 +354,8 @@ int main (int argc, char **argv)
float ratio_representative = DEFAULT_RATIO_REPRESENTATIVE;
unsigned int max_auditionned = DEFAULT_MAX_AUDITIONED;
// Admissible delta between left and right segmentation points
int delta_min = DEFAULT_DELTA_MIN ; // Kmer+Fine
int trim_sequences = DEFAULT_TRIM;
bool delta_min_changed = false;
bool trim_sequences_changed = false;
bool output_sequences_by_cluster = false;
......@@ -398,7 +394,7 @@ int main (int argc, char **argv)
//$$ options: getopt
while ((c = getopt(argc, argv, "A!x:X:hHadI124g:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:m:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:q")) != EOF)
while ((c = getopt(argc, argv, "A!x:X:hHadI124g:V:D:J:k:r:vw:e:E:C:f:W:l:Fc:N:s:b:Sn:o:L%:y:z:uUK3E:t:#:q")) != EOF)
switch (c)
{
......@@ -440,7 +436,6 @@ int main (int argc, char **argv)
case 'D':
f_reps_D.push_back(optarg);
delta_min = DEFAULT_DELTA_MIN_D ;
break;
case 'J':
......@@ -514,11 +509,6 @@ int main (int argc, char **argv)
wmer_size = atoi_NO_LIMIT(optarg);
break;
case 'm':
delta_min = atoi(optarg);
delta_min_changed = true;
break;
case '!':
keep_unsegmented_as_clone = true;
break;
......@@ -838,7 +828,6 @@ int main (int argc, char **argv)
{
try {
multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_REGULAR,
FIRST_IF_UNCHANGED(UNSET_DELTA_MIN, delta_min, delta_min_changed),
FIRST_IF_UNCHANGED("", seed, seed_changed),
FIRST_IF_UNCHANGED(0, trim_sequences, trim_sequences_changed));
} catch (std::exception& e) {
......@@ -853,7 +842,7 @@ int main (int argc, char **argv)
Germline *germline;
germline = new Germline("custom", 'X',
f_reps_V, f_reps_D, f_reps_J,
delta_min, seed, trim_sequences);
seed, trim_sequences);
germline->new_index(indexType);
......@@ -874,14 +863,14 @@ int main (int argc, char **argv)
}
if (multi_germline_unexpected_recombinations_12) {
Germline *pseudo = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, DEFAULT_DELTA_MIN, "", trim_sequences);
Germline *pseudo = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, "", trim_sequences);
pseudo->seg_method = SEG_METHOD_MAX12 ;
pseudo->index = multigermline->index ;
multigermline->germlines.push_back(pseudo);
}
if (multi_germline_unexpected_recombinations_1U) {
Germline *pseudo_u = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, DEFAULT_DELTA_MIN, "", trim_sequences);
Germline *pseudo_u = new Germline(PSEUDO_UNEXPECTED, PSEUDO_UNEXPECTED_CODE, "", trim_sequences);
pseudo_u->seg_method = SEG_METHOD_MAX1U ;
// TODO: there should be more up/downstream regions for the PSEUDO_UNEXPECTED germline. And/or smaller seeds ?
pseudo_u->index = multigermline->index ;
......@@ -892,7 +881,6 @@ int main (int argc, char **argv)
{
for (pair <string, string> path_file: multi_germline_paths_and_files)
multigermline->build_from_json(path_file.first, path_file.second, GERMLINES_INCOMPLETE,
FIRST_IF_UNCHANGED(UNSET_DELTA_MIN, delta_min, delta_min_changed),
FIRST_IF_UNCHANGED("", seed, seed_changed),
FIRST_IF_UNCHANGED(0, trim_sequences, trim_sequences_changed));
if ((! multigermline->one_index_per_germline) && (command != CMD_GERMLINES)) {
......
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