Commit a2898925 authored by Mathieu Giraud's avatar Mathieu Giraud

core/representative.h, vidjil.cpp: RandomScore by default

see #3866
parent ed299a22
......@@ -14,7 +14,7 @@ using namespace std;
#define THRESHOLD_BAD_COVERAGE .5 /* Threshold below which the representatie
coverage is considered bad */
static ReadQualityScore DEFAULT_READ_SCORE;
static RandomScore DEFAULT_READ_SCORE;
/**
* Compute a representative sequence from a list of sequences.
......
......@@ -471,12 +471,12 @@ int main (int argc, char **argv)
-> group(group);
VirtualReadScore *readScorer = &DEFAULT_READ_SCORE;
RandomScore randomScore;
app.add_flag_function("--consensus-on-random-sample",
[&readScorer, &randomScore](size_t n) {
ReadQualityScore readQualityScore;
app.add_flag_function("--consensus-on-longest-sequences",
[&readScorer, &readQualityScore](size_t n) {
UNUSED(n);
readScorer = &randomScore;
}, "for large clones, use a random sample of reads to compute the consensus sequence (instead of a sample of the longest and highest quality reads)")
readScorer = &readQualityScore;
}, "for large clones, use a sample of the longest and highest quality reads to compute the consensus sequence (instead of a random sample)")
->group(group) -> level();
// ----------------------------------------------------------------------------------------------------------------------
......
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