X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffinfocommand.cpp;h=c80ac2e51859331f17f02bcdf5abdd3f89bec6f3;hp=a1b7066482b973bcbaeebefdc718c5c96d70aae9;hb=615301e57c25e241356a9c2380648d117709458d;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index a1b7066..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;
@@ -1039,7 +1055,11 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
         
         if (trim) {
             if(header.clipQualRight < header.clipQualLeft){
-                seq = "NNNN";
+                if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
             }
             else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1050,11 +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]);  }
             }
         }
         
@@ -1235,10 +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';  }
@@ -1260,7 +1282,11 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
 		
         if (trim) {
 			if(header.clipQualRight < header.clipQualLeft){
-				seq = "NNNN";
+				if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
 			}
 			else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 				seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1271,11 +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]);  }
 			}
 		}
 		
@@ -1296,8 +1323,13 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 		
 		if (trim) {
 			if(header.clipQualRight < header.clipQualLeft){
-				out << ">" << header.name << " xy=" << header.xy << endl;
-				out << "0\t0\t0\t0";
+                if (header.clipQualRight == 0) { //don't trim right
+                    out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+                    for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';	}	
+                }else {
+                    out << ">" << header.name << " xy=" << header.xy << endl;
+                    out << "0\t0\t0\t0";
+                }
 			}
 			else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 				out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
@@ -1325,15 +1357,21 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 	try {
-		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;
@@ -1641,7 +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;  }
 					}