Skip to content
Snippets Groups Projects
Commit c795f08e authored by Aaron's avatar Aaron
Browse files

Updated the help message for fastaFromBed

	- Added the -name parameter.  It was missing, so users had no idea it existed.
parent 400b35b6
No related branches found
No related tags found
No related merge requests found
......@@ -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;
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment