added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 9ad287b68d8457e6dffd6e101bbca007c64745eb..85b0b38c8daab23e44c5c676ed1f38009afb7a62 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -22,14 +22,14 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
                vector<int> t;          t.resize(seqs[0]->getAligned().length(), 0);
                vector<int> g;          g.resize(seqs[0]->getAligned().length(), 0);
                vector<int> c;          c.resize(seqs[0]->getAligned().length(), 0);
-               
+       
                filterString = (string(seqs[0]->getAligned().length(), '1'));
                
                //for each sequence
                for (int i = 0; i < seqs.size(); i++) {
                
                        string seqAligned = seqs[i]->getAligned();
-                       
+               
                        for (int j = 0; j < seqAligned.length(); j++) {
                                //if this spot is a gap
                                if ((seqAligned[j] == '-') || (seqAligned[j] == '.'))   {       gaps[j]++;      }
@@ -47,10 +47,8 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
                        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';  numColRemoved++;  }
-                       //cout << "a = " << a[i] <<  " t = " << t[i] <<  " g = " << g[i] <<  " c = " << c[i] << endl;
+                       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();
                return filterString;
@@ -95,7 +93,7 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                openInputFile(file, in);
                vector<Sequence*> container;
                int count = 0;
-               int length = 0;
+               length = 0;
                unaligned = false;
                
                //read in seqs and store in vector