Commit 6d1b5a10 authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: enable filtering by defaut, -Z 3

Thanks to the work by @boreec, we now enable by default
the filtering for the second pass of the clone analysis.

When the computing time is dominated by the FineSegmenter
(such as with '-c clones -z 10000' or '-c segment'),
we get final speed-ups between 2x and 15x (#2360).

We could even set -Z 1 in most of the cases, but it should
be coupled with #3225. See also #3297 and #3344.

Close #3298.
parent 67e6e1b1
Pipeline #32173 failed with stages
in 92 minutes and 41 seconds
......@@ -111,7 +111,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_MAX_AUDITIONED 2000
#define DEFAULT_RATIO_REPRESENTATIVE 0.5
#define DEFAULT_KMER_THRESHOLD NO_LIMIT_VALUE
#define DEFAULT_KMER_THRESHOLD 3
#define DEFAULT_EPSILON 0
#define DEFAULT_MINPTS 10
......@@ -467,7 +467,7 @@ int main (int argc, char **argv)
int kmer_threshold = DEFAULT_KMER_THRESHOLD;
app.add_option("-Z", kmer_threshold,
"typical number of V genes, selected by k-mer comparison, to compare to the read ('" NO_LIMIT "': all genes, default)", false)
"typical number of V genes, selected by k-mer comparison, to compare to the read ('" NO_LIMIT "': all genes)", true)
-> group(group) -> transform(string_NO_LIMIT) -> level();
bool detect_CDR3 = false;
......
  • Le -Z 3 m'avait échappé. Ne pourrait-on pas prendre une marge de sécurité plus importante en attendant #3225 (closed) ?

  • Euh... maintenant tous les tests passent... j'ai essayé d'être très méchant avec #3297, à l'époque je voulais mettre -Z 5 plutôt que -Z 1, et donc 3 est un compromis. Je pense qu'on peut laisser (sauf preuve du contraire sur séquence difficile).

  • Il n'a jamais été question de mettre -Z 1 sans #3225 (closed).

    Je sais que les tests passent, je parle justement de marge de sécurité car il n'y a pas #3225 (closed) pour nous en donner une

    Edited by Mikaël Salson
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