Commit 491572c1 authored by Mikaël Salson's avatar Mikaël Salson
Browse files

{dynprog,vidjil}.cpp: Solve inconsistencies in cost order

We displayed the homopolymer cost before the del_end but actually when
building it we needed the del_end before the homopolymer costs
parent bd34576a
......@@ -105,8 +105,8 @@ ostream& operator<<(ostream& out, const Cost& cost)
out << "\"" << cost.match
<< ", " << cost.mismatch
<< ", " << cost.insertion
<< ", " << cost.homopolymer
<< ", " << cost.deletion_end
<< ", " << cost.homopolymer
<< "\"" ;
return out;
......
......@@ -4,7 +4,7 @@ $ License
1:Vidjil is free software
$ Check default costs
1:segmenter .* "4, -6, -10, -10, -1"
1:segmenter .* "4, -6, -10, -1, -10"
1:clustering .* "1, -4, -4, 0, 0"
......@@ -216,7 +216,7 @@ void usage(char *progname, bool advanced)
if (advanced)
cerr << "Fine segmentation options (second pass)" << endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (default "<< DEFAULT_SEGMENT_COST <<" )"<< endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_SEGMENT_COST <<" )"<< endl
<< " -E <float> maximal e-value for determining if a D segment can be trusted (default: " << THRESHOLD_NB_EXPECTED_D << ")" << endl
<< endl ;
......@@ -231,7 +231,7 @@ void usage(char *progname, bool advanced)
<< " -N <int> minimum required neighbors for automatic clustering (default " << DEFAULT_MINPTS << ")" << endl
<< " -S generate and save comparative matrix for clustering" << endl
<< " -L load comparative matrix for clustering" << endl
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, homo, del_end\" (default "<< DEFAULT_CLUSTER_COST <<" )"<< endl
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_CLUSTER_COST <<" )"<< endl
<< endl ;
cerr << "Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)" << endl
......
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