diff --git a/src/complementBed/complementMain.cpp b/src/complementBed/complementMain.cpp index f70f6c9bfd24ca1babdccccdb183f0afbeb3a15a..3097c8ce113b1173ee084b49673a447f0055688a 100755 --- a/src/complementBed/complementMain.cpp +++ b/src/complementBed/complementMain.cpp @@ -90,12 +90,11 @@ void ShowHelp(void) { cerr << "Description: Returns the base pair complement of a BED file." << endl << endl; cerr << "***NOTE: Only BED3 - BED6 formats allowed.***"<< endl << endl; - cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed>" << endl << endl; + cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <input.bed> -g <genome.txt>" << endl << endl; - //cerr << "OPTIONS: " << endl; - //cerr << "\t" << "-n\t\t\t" << "Report the number of BED entries that were merged. (=1 if no merging occured)" << endl; - //cerr << "\t" << "-d\t\t\t" << "Maximum distance between features that will be merged. (Default is 0)" << endl; - //cerr << "\t\t\t\t" << "For example, \"-d 50\" will merge features that are <= 50 bp apart." << endl << endl; + cerr << "NOTES: " << endl; + cerr << "\t" << "-i stdin\t\t" << "Allows complementBed to read BED from stdin. E.g.: cat a.bed | complementBed -i stdin" << endl << endl; + // end the program here exit(1);