warn about -g when using BAM input in genomecov
@@ -184,6 +184,10 @@ int genomecoverage_main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
showHelp = true;
}
+ // make sure we have both input files
+ if (bamInput && haveGenome) {
+ cerr << endl << "*****" << endl << "*****WARNING: Genome (-g) files are ignored when BAM input is provided. " << endl << "*****" << endl;
+ }
if (bedGraph && eachBase) {
cerr << endl << "*****" << endl << "*****ERROR: Use -d/-dz or -bg, not both" << endl << "*****" << endl;
showHelp = true;
