X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=4e72a960a7bb07d4e94df795bea462519f6d777a;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=0fdf6fce6647269d476945031255bb585e78ba83;hpb=01b7dae5525a480d31a1de5bc273692726da8570;p=mothur.git diff --git a/sffinfocommand.h b/sffinfocommand.h index 0fdf6fc..4e72a96 100644 --- a/sffinfocommand.h +++ b/sffinfocommand.h @@ -17,7 +17,7 @@ struct CommonHeader { unsigned int magicNumber; string version; - unsigned long int indexOffset; + unsigned long long indexOffset; unsigned int indexLength; unsigned int numReads; unsigned short headerLength; @@ -64,13 +64,18 @@ class SffInfoCommand : public Command { public: SffInfoCommand(string); SffInfoCommand(); - ~SffInfoCommand(); - vector getRequiredParameters(); - vector getValidParameters(); - vector getRequiredFiles(); - map > getOutputFiles() { return outputTypes; } - int execute(); - void help(); + ~SffInfoCommand(){} + + vector setParameters(); + string getCommandName() { return "sffinfo"; } + string getCommandCategory() { return "Sequence Processing"; } + string getOutputFileNameTag(string, string); + string getHelpString(); + string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; } + string getDescription() { return "extract sequences reads from a .sff file"; } + + int execute(); + void help() { m->mothurOut(getHelpString()); } private: string sffFilename, sfftxtFilename, outputDir, accnosName; @@ -78,8 +83,7 @@ private: bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos; int mycount; set seqNames; - map > outputTypes; - + //extract sff file functions int extractSffInfo(string, string); int readCommonHeader(ifstream&, CommonHeader&); @@ -95,7 +99,8 @@ private: int printQualSeqData(ofstream&, seqRead&, Header&); int readAccnosFile(string); int parseSffTxt(); - + bool sanityCheck(Header&, seqRead&); + //parsesfftxt file functions int parseHeaderLineToInt(ifstream&); vector parseHeaderLineToFloatVector(ifstream&, int);