Commit 48ba0192 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/2076-help-costs' into 'dev'

Feature a/2076 help costs

Closes #2076

See merge request !108
parents a7e154fc a85080bf
......@@ -90,6 +90,7 @@ void Cost::estimate_K_lambda()
ostream& operator<<(ostream& out, const Cost& cost)
{
if (cost.debug)
out << "(" << cost.match
<< ", " << cost.mismatch
<< "/" << cost.insertion
......@@ -100,6 +101,13 @@ ostream& operator<<(ostream& out, const Cost& cost)
<< ", " << cost.homopolymer
<< ") "
<< cost.K << "/" << cost.lambda ;
else
out << "\"" << cost.match
<< ", " << cost.mismatch
<< ", " << cost.insertion
<< ", " << cost.homopolymer
<< ", " << cost.deletion_end
<< "\"" ;
return out;
}
......
......@@ -26,6 +26,8 @@ typedef struct {
class Cost
{
public:
bool debug = false;
int match;
int mismatch;
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -H 2> out-v ; cat out-v
$ License
1:Vidjil is free software
$ Check default costs
1:segmenter .* "4, -6, -10, -2, -1"
1:clustering .* "1, -4, -4, 0, 0"
......@@ -124,6 +124,7 @@ int main(int argc, char** argv)
// Cost
Cost dpCost = getCost(cost);
dpCost.debug = true ;
cout << "Cost: " << dpCost << endl;
cout << endl;
......
......@@ -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 "<<VDJ<<" )"<< endl
<< " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (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 "<<Cluster<<" )"<< endl
<< " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, homo, del_end\" (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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