changing command name classify.shared to classifyrf.shared

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 3961802804f02c5d60c2a017803b666f43e74047..c80ac2e51859331f17f02bcdf5abdd3f89bec6f3 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -646,7 +646,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        char buffer3 [4];
                        in.read(buffer3, 4);
                        header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
-                       
+            
                        //read num reads
                        char buffer4 [4];
                        in.read(buffer4, 4);
@@ -741,9 +741,19 @@ int SffInfoCommand::adjustCommonHeader(CommonHeader header){
         in.read(mybuffer,8);
         for (int i = 0; i < filehandlesHeaders.size(); i++) {  
             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
+                unsigned long long offset = 0;
+                char* thisbuffer = new char[8];
+                thisbuffer[0] = (offset >> 56) & 0xFF;
+                thisbuffer[1] = (offset >> 48) & 0xFF;
+                thisbuffer[2] = (offset >> 40) & 0xFF;
+                thisbuffer[3] = (offset >> 32) & 0xFF;
+                thisbuffer[4] = (offset >> 24) & 0xFF;
+                thisbuffer[5] = (offset >> 16) & 0xFF;
+                thisbuffer[6] = (offset >> 8) & 0xFF;
+                thisbuffer[7] = offset & 0xFF;
                 ofstream out;
                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
-                out.write(mybuffer, in.gcount()); 
+                out.write(thisbuffer, 8);
                 out.close();
             }
         }
@@ -757,7 +767,13 @@ int SffInfoCommand::adjustCommonHeader(CommonHeader header){
             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
                 ofstream out;
                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
-                out.write(mybuffer, in.gcount()); 
+                int offset = 0;
+                char* thisbuffer = new char[4];
+                thisbuffer[0] = (offset >> 24) & 0xFF;
+                thisbuffer[1] = (offset >> 16) & 0xFF;
+                thisbuffer[2] = (offset >> 8) & 0xFF;
+                thisbuffer[3] = offset & 0xFF;
+                out.write(thisbuffer, 4);
                 out.close();
             }
         }
@@ -871,7 +887,7 @@ int SffInfoCommand::adjustCommonHeader(CommonHeader header){
         for (int i = 0; i < filehandlesHeaders.size(); i++) { 
             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
                 ofstream out;
-                m->openOutputFileAppend(filehandlesHeaders[i][j], out);
+                m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
                 out.write(mybuffer, spot-spotInFile); 
                 out.close();
             }
@@ -920,7 +936,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                        char buffer5 [2];
                        in.read(buffer5, 2);
                        header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
-                       
+            
                        //read clipAdapterLeft
                        char buffer6 [2];
                        in.read(buffer6, 2);
@@ -989,7 +1005,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                 char * mybuffer;
                 mybuffer = new char [spot-startSpotInFile];
                 ifstream in2;
-                m->openInputFile(currentFileName, in2);
+                in2.open(currentFileName.c_str(), ios::binary);
                 in2.seekg(startSpotInFile);
                 in2.read(mybuffer,spot-startSpotInFile);
                 in2.close();
@@ -999,7 +1015,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                                 
                 if(trashCodeLength == 0){
                     ofstream out;
-                    m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
+                    m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
                     out.write(mybuffer, in2.gcount()); 
                     out.close();
                     delete[] mybuffer;
@@ -1007,7 +1023,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                                }
                                else{
                                        ofstream out;
-                    m->openOutputFileAppend(noMatchFile, out);
+                    m->openOutputFileBinaryAppend(noMatchFile, out);
                     out.write(mybuffer, in2.gcount()); 
                     out.close();
                     delete[] mybuffer;
@@ -1343,7 +1359,10 @@ int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& heade
        try {
         
         int endValue = header.clipQualRight;
-        if (header.clipQualRight == 0) {  endValue = read.flowIndex.size(); }
+        if (header.clipQualRight == 0) {
+            endValue = read.flowIndex.size();
+            if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
+        }
         if(endValue > header.clipQualLeft){
             
             int rightIndex = 0;