Commit 068cc3ab authored by arq5x's avatar arq5x
Browse files

deprecate -abam and update help to show that -a supports BAM

parent b561cf55
......@@ -46,14 +46,15 @@ void intersect_help(void) {
cerr << "Version: " << VERSION << "\n";
cerr << "Summary: Report overlaps between two feature files." << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>" << endl << endl;
cerr << "\t\t" << "Note: -b may be followed with multiple databases and/or " << endl;
cerr << "\t\t" "wildcard (*) character(s). " << endl;
cerr << "Options: " << endl;
cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
// -abam is obsolete.
// cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
......
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