X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffinfocommand.cpp;h=c80ac2e51859331f17f02bcdf5abdd3f89bec6f3;hp=0148ab19f407b91d293eebb547927d4c381fd6d0;hb=615301e57c25e241356a9c2380648d117709458d;hpb=567e4bca5d62bd8ea316ce5def320d070d7507b8 diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp index 0148ab1..c80ac2e 100644 --- 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; @@ -1656,7 +1679,7 @@ bool SffInfoCommand::readOligos(string oligoFile){ // get rest of line in case there is a primer name while (!inOligos.eof()) { char c = inOligos.get(); - if (c == 10 || c == 13){ break; } + if (c == 10 || c == 13 || c == -1){ break; } else if (c == 32 || c == 9){;} //space or tab else { group += c; } }