Commit 034ac740 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp, core/tools.{h,cpp}: remove deprecated NO_SPACED_SEEDS

Close #3294.
parent 63035e52
Pipeline #29750 passed with stages
in 49 seconds
......@@ -27,10 +27,6 @@ string spaced(const string &input, const string &seed) {
// return input.substr(0, 7) + input.substr(8, 7);
// #endif
#ifdef NO_SPACED_SEEDS
return input ;
#endif
int j = 0 ;
// cout << input << endl << seed << endl ;
......
......@@ -73,10 +73,6 @@ string spaced(const string &input, const string &seed);
inline int spaced_int(int *input, const string &seed) {
#ifdef NO_SPACED_SEEDS
return input ;
#endif
// cout << input << endl << seed << endl ;
// assert(input.length() == seed.length()); // length is not equal, pointer
......
......@@ -365,11 +365,10 @@ int main (int argc, char **argv)
// ----------------------------------------------------------------------------------------------------------------------
group = "Recombination detection (\"window\" prediction, first pass)";
#ifndef NO_SPACED_SEEDS
group += " (use either -s or -k option, but not both)\n (all these options, except -w, are overriden when using -g)";
#endif
group += "\n (use either -s or -k option, but not both)";
group += "\n (using -k option is equivalent to set with -s a contiguous seed with only '#' characters)" ;
group += "\n (all these options, except -w, are overriden when using -g)";
app.add_flag_function("-q",
[&](size_t n) { indexType = AC_AUTOMATON; },
"use Aho-Corasick-like automaton (experimental)")
......@@ -389,10 +388,6 @@ int main (int argc, char **argv)
"k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)")
-> group(group) -> level() -> set_type_name("INT");
#ifndef NO_SPACED_SEEDS
// << " (using -k option is equivalent to set with -s a contiguous seed with only '#' characters)" << endl
#endif
app.add_option("-w", wmer_size,
"w-mer size used for the length of the extracted window ('" NO_LIMIT "': use all the read, no window clustering)")
-> group(group) -> level() -> transform(string_NO_LIMIT);
......@@ -421,12 +416,6 @@ int main (int argc, char **argv)
"spaced seeds used for the V/J affectation (default: depends on germline)")
-> group(group) -> level();
/*
#ifdef NO_SPACED_SEEDS
cerr << "To enable the option -s, please compile without NO_SPACED_SEEDS" << endl;
#endif
*/
// ----------------------------------------------------------------------------------------------------------------------
group = "Recombination detection, experimental options (do not use)";
......@@ -657,26 +646,12 @@ int main (int argc, char **argv)
size_t min_cover_representative = (size_t) (min_reads_clone < (int) max_auditionned ? min_reads_clone : max_auditionned) ;
// Default seeds
#ifdef NO_SPACED_SEEDS
if (! seed_changed)
{
cerr << ERROR_STRING << PROGNAME << " was compiled with NO_SPACED_SEEDS: please provide a -k option." << endl;
return 1;
}
#endif
#ifndef NO_SPACED_SEEDS
// Check seed buffer
if (seed.size() >= MAX_SEED_SIZE)
{
cerr << ERROR_STRING << "Seed size is too large (MAX_SEED_SIZE)." << endl ;
return 1;
}
#endif
if ((wmer_size< 0) && (wmer_size!= NO_LIMIT_VALUE))
{
......
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