X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimera.cpp;h=4ae4991c8d78ebe7a90920972175554dd83b6d36;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=75e81c076a9ce113ff26e1d62027b86b16571527;hpb=6d7408400b6bbdde4173922c5dca528f9f4e0a22;p=mothur.git

diff --git a/chimera.cpp b/chimera.cpp
index 75e81c0..4ae4991 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 {
 		
@@ -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();
@@ -88,13 +90,21 @@ vector<Sequence*> Chimera::readSeqs(string file) {
 		ifstream in;
 		openInputFile(file, in);
 		vector<Sequence*> container;
+		int count = 0;
+		int length = 0;
+		unaligned = false;
 		
 		//read in seqs and store in vector
 		while(!in.eof()){
 			
-			Sequence* current = new Sequence(in);
-			container.push_back(current);
-			gobble(in);
+			Sequence* current = new Sequence(in);  gobble(in);
+			
+			if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+			else if (length != current->getAligned().length()) { //seqs are unaligned
+				unaligned = true;
+			}
+			
+			if (current->getName() != "") {  container.push_back(current);  }
 		}
 		
 		in.close();
@@ -142,6 +152,10 @@ 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; 
 		
@@ -149,7 +163,7 @@ 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);