This is v.1.4.0

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 064189b1423434f24e88fb05df3ad67a7ea4967f..4bf18d7712276da69d5fc4eb488bc249a213d9c7 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -193,7 +193,7 @@ int AlignCommand::execute(){
                        
                        while(!inFASTA.eof()){
                                char c = inFASTA.get();
-                               if(c == '>'){   positions.push_back(inFASTA.tellg());   }
+                               if(c == '>'){   int pos = inFASTA.tellg(); positions.push_back(pos-1);  }
                                while (!inFASTA.eof())  {       c = inFASTA.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
                        }
                        inFASTA.close();
@@ -343,22 +343,15 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName)
 void AlignCommand::appendAlignFiles(string temp, string filename) {
        try{
                
-               //open output file in append mode
                ofstream output;
-               openOutputFileAppend(filename, output);
-               
-               //open temp file for reading
                ifstream input;
+               openOutputFileAppend(filename, output);
                openInputFile(temp, input);
                
-               string line;
-               //read input file and write to output file
-               while(input.eof() != true) {
-                       getline(input, line); //getline removes the newline char
-                       if (line != "") {
-                               output << line << endl;   // Appending back newline char 
-                       }
-               }       
+               while(char c = input.get()){
+                       if(input.eof())         {       break;                  }
+                       else                            {       output << c;    }
+               }
                
                input.close();
                output.close();
@@ -378,23 +371,17 @@ void AlignCommand::appendAlignFiles(string temp, string filename) {
 void AlignCommand::appendReportFiles(string temp, string filename) {
        try{
                
-               //open output file in append mode
                ofstream output;
-               openOutputFileAppend(filename, output);
-               
-               //open temp file for reading
                ifstream input;
+               openOutputFileAppend(filename, output);
                openInputFile(temp, input);
+
                while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
-               
-               string line;
-               //read input file and write to output file
-               while(input.eof() != true) {
-                       getline(input, line); //getline removes the newline char
-                       if (line != "") {
-                               output << line << endl;   // Appending back newline char 
-                       }
-               }       
+                               
+               while(char c = input.get()){
+                       if(input.eof())         {       break;                  }
+                       else                            {       output << c;    }
+               }
                
                input.close();
                output.close();