modifications to commands to add headers to list file.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 3961802804f02c5d60c2a017803b666f43e74047..399f253570feaefcd39f979a0af2b7f3c5bb8632 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -559,6 +559,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
                        if (m->control_pressed) { count = 0; break;   }
                        
                        if (count >= header.numReads) { break; }
+            //if (count >= 100) { break; }
                }
                
                //report progress
@@ -646,11 +647,13 @@ 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);
                        header.numReads =  be_int4(*(unsigned int *)(&buffer4));
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: numReads = " + toString(header.numReads) + "\n"); }
                                
                        //read header length
                        char buffer5 [2];
@@ -716,7 +719,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -729,7 +732,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -741,9 +744,19 @@ 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()); 
+                m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
+                out.write(thisbuffer, 8);
                 out.close();
             }
         }
@@ -756,8 +769,14 @@ 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);
-                out.write(mybuffer, in.gcount()); 
+                m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
+                unsigned 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();
             }
         }
@@ -770,13 +789,20 @@ 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);
                 //convert number of reads to 4 byte char*
                 char* thisbuffer = new char[4];
-                thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
-                thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
-                thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
-                thisbuffer[3] = numSplitReads[i][j] & 0xFF;
+                if ((m->findEdianness()) == "BIG_ENDIAN") {
+                    thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
+                    thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
+                    thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
+                    thisbuffer[3] = numSplitReads[i][j] & 0xFF;
+                }else {
+                    thisbuffer[0] = numSplitReads[i][j] & 0xFF;
+                    thisbuffer[1] = (numSplitReads[i][j] >> 8) & 0xFF;
+                    thisbuffer[2] = (numSplitReads[i][j] >> 16) & 0xFF;
+                    thisbuffer[3] = (numSplitReads[i][j] >> 24) & 0xFF;
+                 }
                 out.write(thisbuffer, 4);
                 out.close();
                 delete[] thisbuffer;
@@ -789,7 +815,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -802,7 +828,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -815,7 +841,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -828,7 +854,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -841,7 +867,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -854,7 +880,7 @@ 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, in.gcount()); 
                 out.close();
             }
@@ -871,7 +897,7 @@ 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();
             }
@@ -897,7 +923,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
             
             //read header length
                        char buffer [2];
-                       in.read(buffer, 2);
+                       in.read(buffer, 2); 
                        header.headerLength = be_int2(*(unsigned short *)(&buffer));
             
                        //read name length
@@ -909,33 +935,39 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                        char buffer3 [4];
                        in.read(buffer3, 4);
                        header.numBases =  be_int4(*(unsigned int *)(&buffer3));
+            
                        
                        //read clip qual left
                        char buffer4 [2];
                        in.read(buffer4, 2);
                        header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
-                       header.clipQualLeft = 5; 
+                       header.clipQualLeft = 5;
+            
                        
                        //read clip qual right
                        char buffer5 [2];
                        in.read(buffer5, 2);
                        header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
-                       
+           
+            
                        //read clipAdapterLeft
                        char buffer6 [2];
                        in.read(buffer6, 2);
                        header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
             
+            
                        //read clipAdapterRight
                        char buffer7 [2];
                        in.read(buffer7, 2);
                        header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
             
+            
                        //read name
                        char* tempBuffer = new char[header.nameLength];
                        in.read(&(*tempBuffer), header.nameLength);
                        header.name = tempBuffer;
                        if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
+            
                        delete[] tempBuffer;
                        
                        //extract info from name
@@ -989,7 +1021,7 @@ 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();
@@ -998,21 +1030,21 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, H
                 int trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex);
                                 
                 if(trashCodeLength == 0){
+                    //cout << header.name << " length = " << spot << '\t' << startSpotInFile << '\t' << in2.gcount() << endl;
+                    
                     ofstream out;
-                    m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
+                    m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
                     out.write(mybuffer, in2.gcount()); 
                     out.close();
-                    delete[] mybuffer;
                     numSplitReads[barcodeIndex][primerIndex]++;
                                }
                                else{
                                        ofstream out;
-                    m->openOutputFileAppend(noMatchFile, out);
+                    m->openOutputFileBinaryAppend(noMatchFile, out);
                     out.write(mybuffer, in2.gcount()); 
                     out.close();
-                    delete[] mybuffer;
                                }
-                               
+                               delete[] mybuffer;
                        }
                }else{
                        m->mothurOut("Error reading."); m->mothurOutEndLine();
@@ -1343,7 +1375,10 @@ 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;
@@ -1752,7 +1787,7 @@ bool SffInfoCommand::readOligos(string oligoFile){
                                        }
                                        
                                        filehandles[itBar->second][itPrimer->second] = thisFilename;
-                                       m->openOutputFile(thisFilename, temp);          temp.close();
+                                       temp.open(thisFilename.c_str(), ios::binary);           temp.close();
                                }
                        }
                }