diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp index 0facc5e4976a410293c33f16a85afd9da920a38a..3385a6587c9f457437ae81e6675f2804e3aa5ff5 100755 --- a/src/fastaFromBed/fastaFromBedMain.cpp +++ b/src/fastaFromBed/fastaFromBedMain.cpp @@ -83,8 +83,6 @@ int main(int argc, char* argv[]) { Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile, bedFile, fastaOutFile); b2f->ExtractDNA(); - - cerr << PROGRAM_NAME << " completed." << endl; return 0; } else { @@ -101,7 +99,7 @@ void ShowHelp(void) { cerr << "===============================================" << endl << endl; cerr << "Description: Extract DNA sequences into a fasta file based on BED coordinates." << endl << endl; - cerr << "Usage: " << PROGRAM_NAME << " -db <fasta db file> -bed <bed coordinates file> -fo <output fasta file w/ requested DNA>" << endl << endl; + cerr << "Usage: " << PROGRAM_NAME << " -db -bed -fo -name" << endl << endl; cerr << "Input Files:" << endl; cerr << " -db <FASTA db file> " << endl; @@ -110,6 +108,9 @@ void ShowHelp(void) { cerr << "Output Files:" << endl; cerr << " -fo <FASTA output file> " << endl; + cerr << "Options:" << endl; + cerr << " -name Use the BED name field (#4) for the FASTA header " << endl; + cerr << "\nHelp:" << endl; cerr << " -h shows this help text" << endl;