started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstr...

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 6ec24d155263e86951ed600ac59cbbe05c932581..8851b755a09a0b030418e7881d09caedb4753584 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -10,7 +10,7 @@
 #include "chimera.h"
 
 //***************************************************************************************************************
-//this is a vertical filter
+//this is a vertical soft filter
 void Chimera::createFilter(vector<Sequence*> seqs) {
        try {
                
@@ -40,6 +40,7 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
                        }
                }
                
+               //zero out spot where all sequences have blanks
                //zero out spot where all sequences have blanks
                int numColRemoved = 0;
                for(int i = 0;i < seqs[0]->getAligned().length(); i++){
@@ -48,6 +49,7 @@ void Chimera::createFilter(vector<Sequence*> seqs) {
                        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();