Commit bd34576a authored by Mikaël Salson's avatar Mikaël Salson
Browse files

dynprog.h: Don't have a specific homopolymer cost

See #2851 for the reasons why
parent 932e1eb1
...@@ -74,8 +74,8 @@ const Cost Levenshtein = Cost(0, -1, -1); ...@@ -74,8 +74,8 @@ const Cost Levenshtein = Cost(0, -1, -1);
const Cost DNA = Cost(+5, -4, -10); const Cost DNA = Cost(+5, -4, -10);
// Vidjil costs // Vidjil costs
const Cost VDJ = Cost(+4, -6, -10, -1, -2); const Cost VDJ = Cost(+4, -6, -10, -1);
const Cost VDJaffine = Cost(+4, -6, -15, -1, -1, -2); const Cost VDJaffine = Cost(+4, -6, -15, -1, -1, MINUS_INF);
const Cost IdentityDirty = Cost(+1000, -1, -1); // pour avoir une estimation de longueur de l'alignement, utilise dans compare-all const Cost IdentityDirty = Cost(+1000, -1, -1); // pour avoir une estimation de longueur de l'alignement, utilise dans compare-all
const Cost Cluster = Cost(+1, -4, -4, 0, 0); const Cost Cluster = Cost(+1, -4, -4, 0, 0);
......
!LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_DATA/msa.fa !LAUNCH: $VIDJIL_DIR/algo/tools/align -m 6 -i 0 -j 1 $VIDJIL_DATA/msa.fa
$ Default cost and parameters $ Default cost and parameters
1: (4, -6/-10/-10, -9999-9999/-9999-9999, -1, -2) 1: (4, -6/-10/-10, -9999-9999/-9999-9999, -1, -10)
1: 0.05/0.34 1: 0.05/0.34
$ Global alignment $ Global alignment
......
...@@ -4,7 +4,7 @@ $ License ...@@ -4,7 +4,7 @@ $ License
1:Vidjil is free software 1:Vidjil is free software
$ Check default costs $ Check default costs
1:segmenter .* "4, -6, -10, -2, -1" 1:segmenter .* "4, -6, -10, -10, -1"
1:clustering .* "1, -4, -4, 0, 0" 1:clustering .* "1, -4, -4, 0, 0"
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