Commit c8ec8a82 authored by Mathieu Giraud's avatar Mathieu Giraud

dnyprog.{h,cpp}, vidjil.cpp: -C/-f, display default cost

parent 9317d175
......@@ -112,6 +112,15 @@ ostream& operator<<(ostream& out, const Cost& cost)
return out;
}
string string_of_cost(const Cost cost)
{
stringstream ss;
ss << cost ;
return ss.str();
}
Cost::Cost()
{
}
......
......@@ -67,6 +67,7 @@ class Cost
ostream& operator<<(ostream& out, const Cost& cost);
string string_of_cost(const Cost cost);
// Usual costs
const Cost Hamming = Cost(0, -1, MINUS_INF);
......
......@@ -417,8 +417,7 @@ int main (int argc, char **argv)
segment_cost = strToCost(res[0].c_str(), VDJ);
return true;
},
"use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default DEFAULT_SEGMENT_COST )"
// TODO: description, default value
"use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default " + string_of_cost(DEFAULT_SEGMENT_COST) + ")"
) -> group(group);
app.add_option("-E", expected_value_D, "maximal e-value for determining if a D segment can be trusted", true) -> group(group) -> level();
......@@ -446,8 +445,7 @@ int main (int argc, char **argv)
cluster_cost = strToCost(res[0].c_str(), Cluster);
return true;
},
"use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default DEFAULT_CLUSTER_COST )"
// TODO: description, default value
"use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default " + string_of_cost(DEFAULT_CLUSTER_COST) + ")"
) -> group(group) -> level();
group = "Limits to report a clone (or a window)";
......
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