diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp index fe87c9f3d96cc6b1b98b69607f6a40affab05597..a9eeb36990267c69e78b473f8824483b75629cb6 100644 --- a/src/mapFile/mapMain.cpp +++ b/src/mapFile/mapMain.cpp @@ -215,6 +215,8 @@ void map_help(void) { cerr << "\t\tthat overlap A on the _opposite_ strand." << endl; cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl; + cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl; + cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl; cerr <<"\t\tacross input files." << endl << endl;