Commit 070ff0d3 authored by arq5x's avatar arq5x
Browse files

update the help for coverage to reflect new role of A versus B.

parent a0778bfc
......@@ -23,14 +23,14 @@ void coverage_help(void) {
cerr << "Options: " << endl;
cerr << "\t-hist\t" << "Report a histogram of coverage for each feature in B" << endl;
cerr << "\t\tas well as a summary histogram for _all_ features in B." << endl << endl;
cerr << "\t\tOutput (tab delimited) after each feature in B:" << endl;
cerr << "\t\t 1) depth\n\t\t 2) # bases at depth\n\t\t 3) size of B\n\t\t 4) % of B at depth" << endl << endl;
cerr << "\t-hist\t" << "Report a histogram of coverage for each feature in A" << endl;
cerr << "\t\tas well as a summary histogram for _all_ features in A." << endl << endl;
cerr << "\t\tOutput (tab delimited) after each feature in A:" << endl;
cerr << "\t\t 1) depth\n\t\t 2) # bases at depth\n\t\t 3) size of A\n\t\t 4) % of A at depth" << endl << endl;
cerr << "\t-d\t" << "Report the depth at each position in each B feature." << endl;
cerr << "\t-d\t" << "Report the depth at each position in each A feature." << endl;
cerr << "\t\tPositions reported are one based. Each position" << endl;
cerr << "\t\tand depth follow the complete B feature." << endl << endl;
cerr << "\t\tand depth follow the complete A feature." << endl << endl;
cerr << "\t-counts\t" << "Only report the count of overlaps, don't compute fraction, etc." << endl << endl;
......
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