X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.cpp;h=01338ca34be42556131b15a0ead73c0ef9952858;hb=fbaa6c7ac44f857c1ece7c8199e9e7e09b4bbe74;hp=885aadc9c05eb34ba16d0dca6e48322dc452e5af;hpb=dfae916a398508554d35c6b3c8002b69becb53be;p=mothur.git

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 885aadc..01338ca 100644
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -54,11 +54,21 @@ SffInfoCommand::SffInfoCommand(string option)  {
 					}
 	
 					ifstream in;
-					int ableToOpen = openInputFile(filenames[i], in);
+					int ableToOpen = openInputFile(filenames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
+							m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							filenames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					if (ableToOpen == 1) { 
-						m->mothurOut(filenames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+						m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 						//erase from file list
 						filenames.erase(filenames.begin()+i);
 						i--;
@@ -84,11 +94,21 @@ SffInfoCommand::SffInfoCommand(string option)  {
 					}
 	
 					ifstream in;
-					int ableToOpen = openInputFile(accnosFileNames[i], in);
+					int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
+							m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							accnosFileNames[i] = tryPath;
+						}
+					}
 					in.close();
 					
 					if (ableToOpen == 1) { 
-						m->mothurOut(accnosFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+						m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 						//erase from file list
 						accnosFileNames.erase(accnosFileNames.begin()+i);
 						i--;
@@ -128,9 +148,16 @@ SffInfoCommand::SffInfoCommand(string option)  {
 
 void SffInfoCommand::help(){
 	try {
-		m->mothurOut("The sffinfo command reads a sff file and outputs a .sff.txt file.\n");
-		
-		m->mothurOut("Example sffinfo(sff=...).\n");
+		m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");
+		m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
+		m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n");
+		m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n");
+		m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n");
+		m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n");
+		m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n");
+		m->mothurOut("The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n");
+		m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");
+		m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
 		m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
 	}
 	catch(exception& e) {
@@ -336,8 +363,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 			if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 				
 			/* Pad to 8 chars */
-			int spotInFile = in.tellg();
-			int spot = (spotInFile + 7)& ~7;  // ~ inverts
+			unsigned long int spotInFile = in.tellg();
+			unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
 			in.seekg(spot);
 			
 		}else{
@@ -399,8 +426,8 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
 			if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 			
 			/* Pad to 8 chars */
-			int spotInFile = in.tellg();
-			int spot = (spotInFile + 7)& ~7;
+			unsigned long int spotInFile = in.tellg();
+			unsigned long int spot = (spotInFile + 7)& ~7;
 			in.seekg(spot);
 			
 		}else{
@@ -451,8 +478,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
 			}
 		
 			/* Pad to 8 chars */
-			int spotInFile = in.tellg();
-			int spot = (spotInFile + 7)& ~7;
+			unsigned long int spotInFile = in.tellg();
+			unsigned long int spot = (spotInFile + 7)& ~7;
 			in.seekg(spot);
 			
 		}else{