added more descriptive error messages to sharedlist

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 8aaab4b12a4c5c261f8a7a4494ca7ef4f12ea923..75e81c076a9ce113ff26e1d62027b86b16571527 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -41,13 +41,16 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
                }
                
                //zero out spot where all sequences have blanks
+               int numColRemoved = 0;
                for(int i = 0;i < seqs[0]->getAligned().length(); i++){
-                       if(gaps[i] == seqs.size())      {       filterString[i] = '0';  }
+                       if(gaps[i] == seqs.size())      {       filterString[i] = '0';  numColRemoved++;  }
                        
-                       else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) {      filterString[i] = '0';  }
+                       else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) {      filterString[i] = '0';  numColRemoved++;  }
                        //cout << "a = " << a[i] <<  " t = " << t[i] <<  " g = " << g[i] <<  " c = " << c[i] << endl;
                }
 //cout << "filter = " << filterString << endl; 
+
+               mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  mothurOutEndLine();
        }
        catch(exception& e) {
                errorOut(e, "Chimera", "createFilter");