X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=4965cfd75e06c9f8ba8157056922514581e3e10e;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=765dc78e68a2ac12034853c008055b87d58abc03;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 765dc78..4965cfd 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -170,7 +170,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
 							//erase from file list
 							filenames.erase(filenames.begin()+i);
 							i--;
-						}
+						}else { m->setSFFFile(filenames[i]); }
 					}
 				}
 				
@@ -283,7 +283,7 @@ SffInfoCommand::SffInfoCommand(string option)  {
 			}
 			
 			if ((sfftxtFilename == "") && (filenames.size() == 0)) {  
-				//if there is a current fasta file, use it
+				//if there is a current sff file, use it
 				string filename = m->getSFFFile(); 
 				if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
@@ -303,7 +303,7 @@ int SffInfoCommand::execute(){
 		
 		for (int s = 0; s < filenames.size(); s++) {
 			
-			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} return 0; }
+			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} return 0; }
 			
 			int start = time(NULL);
 			
@@ -319,7 +319,7 @@ int SffInfoCommand::execute(){
 		
 		if (sfftxtFilename != "") {  parseSffTxt(); }
 		
-		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} return 0; }
+		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} return 0; }
 		
 		//set fasta file as new current fastafile
 		string current = "";
@@ -466,7 +466,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 			//read offset
 			char buffer2 [8];
 			in.read(buffer2, 8);
-			header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
+			header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 			
 			//read index length
 			char buffer3 [4];
@@ -513,8 +513,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 			delete[] tempBuffer2;
 				
 			/* Pad to 8 chars */
-			unsigned long int spotInFile = in.tellg();
-			unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
+			unsigned long long spotInFile = in.tellg();
+			unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 			in.seekg(spot);
 			
 		}else{
@@ -581,8 +581,8 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
 			decodeName(header.timestamp, header.region, header.xy, header.name);
 			
 			/* Pad to 8 chars */
-			unsigned long int spotInFile = in.tellg();
-			unsigned long int spot = (spotInFile + 7)& ~7;
+			unsigned long long spotInFile = in.tellg();
+			unsigned long long spot = (spotInFile + 7)& ~7;
 			in.seekg(spot);
 			
 		}else{
@@ -634,8 +634,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
 			}
 	
 			/* Pad to 8 chars */
-			unsigned long int spotInFile = in.tellg();
-			unsigned long int spot = (spotInFile + 7)& ~7;
+			unsigned long long spotInFile = in.tellg();
+			unsigned long long spot = (spotInFile + 7)& ~7;
 			in.seekg(spot);
 			
 		}else{
@@ -901,13 +901,20 @@ int SffInfoCommand::parseSffTxt() {
 		//output file names
 		ofstream outFasta, outQual, outFlow;
 		string outFastaFileName, outQualFileName;
-		string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "flow";
+		string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
+		if (fileRoot.length() > 0) {
+			//rip off last .
+			fileRoot = fileRoot.substr(0, fileRoot.length()-1);
+			fileRoot = m->getRootName(fileRoot);
+		}
+		
+		string outFlowFileName = outputDir + fileRoot + "flow";
 		if (trim) {
-			outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "fasta";
-			outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "qual";
+			outFastaFileName = outputDir + fileRoot + "fasta";
+			outQualFileName = outputDir + fileRoot + "qual";
 		}else{
-			outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.fasta";
-			outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.qual";
+			outFastaFileName = outputDir + fileRoot + "raw.fasta";
+			outQualFileName = outputDir + fileRoot + "raw.qual";
 		}
 		
 		if (fasta)	{ m->openOutputFile(outFastaFileName, outFasta);	outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }