Commit 038e4146 authored by Mathieu Giraud's avatar Mathieu Giraud

kmeraffect.h: define AFFECT_{UNKNOWN,AMBIGUOUS}_SYMBOL, "_" and "?"

This was hardcoded twice in the code.
parent 1509b803
......@@ -120,9 +120,9 @@ int KmerAffect::getStrand() const{
string KmerAffect::getLabel() const {
if (isUnknown())
return "_";
return AFFECT_UNKNOWN_SYMBOL;
if (isAmbiguous())
return "?";
return AFFECT_AMBIGUOUS_SYMBOL;
return string(1, affect_char(affect));
}
......
......@@ -139,6 +139,10 @@ bool operator>=(const KmerAffect &a1, const KmerAffect &a2);
bool operator!=(const KmerAffect &a1, const KmerAffect &a2);
ostream &operator<<(ostream &os, const KmerAffect &kmer);
#define AFFECT_AMBIGUOUS_SYMBOL "?"
#define AFFECT_UNKNOWN_SYMBOL "_"
/**
* Constant defining the unknown affectation (not known yet)
*/
......
......@@ -676,15 +676,12 @@ int main (int argc, char **argv)
/////////////////////////////////////////
if (command == CMD_GERMLINES)
{
#define KMER_AMBIGUOUS "?"
#define KMER_UNKNOWN "_"
map <char, int> stats_kmer, stats_max;
IKmerStore<KmerAffect> *index = multigermline->index ;
// Initialize statistics, with two additional categories
index->labels.push_back(make_pair(KmerAffect::getAmbiguous(), KMER_AMBIGUOUS));
index->labels.push_back(make_pair(KmerAffect::getUnknown(), KMER_UNKNOWN));
index->labels.push_back(make_pair(KmerAffect::getAmbiguous(), AFFECT_AMBIGUOUS_SYMBOL));
index->labels.push_back(make_pair(KmerAffect::getUnknown(), AFFECT_UNKNOWN_SYMBOL));
for (list< pair <KmerAffect, string> >::const_iterator it = index->labels.begin(); it != index->labels.end(); ++it)
{
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment