added tempdefault to set.dir and fixed bug with padding type in sffinfo.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 37ab0ba8fe01887c026311b7f03838b67dba563f..01338ca34be42556131b15a0ead73c0ef9952858 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -148,9 +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) {
@@ -356,8 +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{
@@ -419,8 +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{
@@ -471,8 +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{