Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

Commit 8f6f8bd1 authored by Mikaël Salson's avatar Mikaël Salson Committed by Mathieu Giraud
Browse files

core/representative: The contiguous seed can be given as a parameter

We may not want to hard-code the contiguous seed (particularly for the tests).
We may also want to provide the spaced seeds, but it is not possible at the
moment. We will see if it appears to be useful.
parent dcc7acea
......@@ -84,11 +84,17 @@ KmerRepresentativeComputer::KmerRepresentativeComputer(list<Sequence> &r,
void KmerRepresentativeComputer::compute(bool try_hard) {
assert(coverage_reference_length > 0);
is_computed = false;
string seed = getSeed();
if (seed.size() == 0)
seed = "##########";
assert(seed.find('-') == string::npos);
// First create an index on the set of reads
IKmerStore<Kmer> *index = new MapKmerStore<Kmer>(getSeed(), revcomp);
string seeds[] = {"##########", // The first seed should be a contiguous seed.
string seeds[] = {seed, // The first seed should be a contiguous seed.
"##-##-##-##-##-",
"#-##-##-##-##-#",
"-##-##-##-##-##",
......
......@@ -105,7 +105,11 @@ protected:
string seed;
int stability_limit;
public:
KmerRepresentativeComputer(list<Sequence> &r, string seed);
/**
* The provided seed must be a contiguous seed. If not provided, the default
* one is used.
*/
KmerRepresentativeComputer(list<Sequence> &r, string seed="");
// Getters, setters
string getSeed() const;
......
......@@ -1358,7 +1358,7 @@ int main (int argc, char **argv)
}
KmerRepresentativeComputer repComp
= windowsStorage->getRepresentativeComputer(it->first, seed,
= windowsStorage->getRepresentativeComputer(it->first, "",
min_cover_representative,
ratio_representative,
max_auditionned);
......
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