Commit e1d6fc15 authored by Mathieu Giraud's avatar Mathieu Giraud

core/windowExtractor.{h,cpp}, vidjil.cpp: do not handle anymore -x/-X options...

core/windowExtractor.{h,cpp}, vidjil.cpp: do not handle anymore -x/-X options inside WindowExtractor
parent e2a2d04b
......@@ -18,23 +18,17 @@ WindowExtractor::WindowExtractor(MultiGermline *multigermline): out_segmented(NU
WindowsStorage *WindowExtractor::extract(OnlineFasta *reads,
size_t w,
map<string, string> &windows_labels, bool only_labeled_windows,
int stop_after, int only_nth_read, bool keep_unsegmented_as_clone,
bool keep_unsegmented_as_clone,
double nb_expected, int nb_reads_for_evalue) {
init_stats();
WindowsStorage *windowsStorage = new WindowsStorage(windows_labels);
windowsStorage->setMaximalNbReadsPerWindow(max_reads_per_window);
int nb_reads_all = 0;
unsigned long long int bp_total = 0;
while (reads->hasNext() && (int) nb_reads != stop_after) {
while (reads->hasNext()) {
reads->next();
nb_reads_all++;
if (nb_reads_all % only_nth_read)
continue ;
nb_reads++;
if (out_affects) {
......
......@@ -56,7 +56,7 @@ class WindowExtractor {
WindowsStorage *extract(OnlineFasta *reads,
size_t w,
map<string, string> &windows_labels, bool only_labeled_windows=false,
int stop_after=-1, int only_nth_reads=1, bool keep_unsegmented_as_clone=false,
bool keep_unsegmented_as_clone=false,
double nb_expected = THRESHOLD_NB_EXPECTED, int nb_reads_for_evalue = 1);
/**
......
......@@ -1031,7 +1031,7 @@ int main (int argc, char **argv)
WindowsStorage *windowsStorage = we.extract(reads, w,
windows_labels, only_labeled_windows,
max_reads_processed, only_nth_read, keep_unsegmented_as_clone,
keep_unsegmented_as_clone,
expected_value, nb_reads_for_evalue);
windowsStorage->setIdToAll();
size_t nb_total_reads = we.getNbReads();
......
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