X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.cpp;h=8851b755a09a0b030418e7881d09caedb4753584;hb=05a0195e07c42c996592ee1c8abb63adedb7f493;hp=8aaab4b12a4c5c261f8a7a4494ca7ef4f12ea923;hpb=f7fbd74ffedcf62217109c22e828453eaefa1458;p=mothur.git

diff --git a/chimera.cpp b/chimera.cpp
index 8aaab4b..8851b75 100644
--- 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 {
 		
@@ -41,13 +41,18 @@ 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++){
-			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");
@@ -139,6 +144,10 @@ vector< vector<float> > Chimera::readQuantiles() {
 		openInputFile(quanfile, in);
 		
 		vector< vector<float> > quan;
+		vector <float> temp; temp.resize(6, 0);
+		
+		//to fill 0
+		quan.push_back(temp); 
 	
 		int num; float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine; 
 		
@@ -146,7 +155,7 @@ vector< vector<float> > Chimera::readQuantiles() {
 			
 			in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine; 
 			
-			vector <float> temp;
+			temp.clear();
 			
 			temp.push_back(ten); 
 			temp.push_back(twentyfive);