working on dereplicate=t issue in chimera.slayer and chimera.perseus, added appendFil...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index f7b0d86bf93ff1c3f1ff6ec4ad62d21d66fc382b..3e4db45bcc43990a18f7d8e51493388d28a6d850 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1170,7 +1170,42 @@ int MothurOut::appendFiles(string temp, string filename) {
                exit(1);
        }       
 }
-
+/**************************************************************************************************/
+int MothurOut::appendFilesWithoutHeaders(string temp, string filename) {
+       try{
+               ofstream output;
+               ifstream input;
+        
+               //open output file in append mode
+               openOutputFileAppend(filename, output);
+               int ableToOpen = openInputFile(temp, input, "no error");
+               //int ableToOpen = openInputFile(temp, input);
+               
+               int numLines = 0;
+               if (ableToOpen == 0) { //you opened it
+        
+            string headers = getline(input); gobble(input);
+            if (debug) { mothurOut("[DEBUG]: skipping headers " + headers +'\n'); }
+            
+            char buffer[4096];
+            while (!input.eof()) {
+                input.read(buffer, 4096);
+                output.write(buffer, input.gcount());
+                //count number of lines
+                for (int i = 0; i < input.gcount(); i++) {  if (buffer[i] == '\n') {numLines++;} }
+            }
+                       input.close();
+               }
+               
+               output.close();
+               
+               return numLines;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "appendFiles");
+               exit(1);
+       }       
+}
 /**************************************************************************************************/
 string MothurOut::sortFile(string distFile, string outputDir){
        try {