changing command name classify.shared to classifyrf.shared

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 911009982a3ed7a3e5da2845094a82b1338b74a3..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;
@@ -1054,11 +1070,12 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
         }else{
             //if you wanted the sfftxt then you already converted the bases to the right case
             if (!sfftxt) {
+                int endValue = header.clipQualRight;
                 //make the bases you want to clip lowercase and the bases you want to keep upper case
-                if(header.clipQualRight == 0){ header.clipQualRight = seq.length();    }
+                if(endValue == 0){     endValue = seq.length();        }
                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
-                for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
-                for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
+                for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
+                for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
             }
         }
         
@@ -1239,10 +1256,11 @@ int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& hea
                for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
                
                //make the bases you want to clip lowercase and the bases you want to keep upper case
-               if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
+        int endValue = header.clipQualRight;
+               if(endValue == 0){      endValue = read.bases.length(); }
                for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
-               for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
-               for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
+               for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
+               for (int i = (endValue-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
                
                out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
                for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
@@ -1279,11 +1297,12 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
                }else{
                        //if you wanted the sfftxt then you already converted the bases to the right case
                        if (!sfftxt) {
+                int endValue = header.clipQualRight;
                                //make the bases you want to clip lowercase and the bases you want to keep upper case
-                               if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
+                               if(endValue == 0){      endValue = seq.length();        }
                                for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
-                               for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
-                               for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
+                               for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
+                               for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
                        }
                }
                
@@ -1338,17 +1357,21 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
-        if (header.clipQualRight == 0) { header.clipQualRight = read.flowgram.size(); }
         
-               if(header.clipQualRight > header.clipQualLeft){
-                       
-                       int rightIndex = 0;
-                       for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
-
-                       out << header.name << ' ' << rightIndex;
-                       for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
-                       out << endl;
-               }
+        int endValue = header.clipQualRight;
+        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;
+            for (int i = 0; i < endValue; i++) {  rightIndex +=  read.flowIndex[i];     }
+            
+            out << header.name << ' ' << rightIndex;
+            for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
+            out << endl;
+        }
                
                
                return 0;