L1_HITS_UPDATE.md

L1 Hits Default Value Update

Summary

Updated the default value for L1-hits (-H) parameter from 1 to 3 in wfmash.

Changes Made

File: src/interface/parse_args.hpp

1. Line 82: Updated help text

   // Before:
   args::ValueFlag<int> min_hits(filtering_opts, "INT", "min hits for L1 filtering [1]", {'H', "l1-hits"});
   
   // After:
   args::ValueFlag<int> min_hits(filtering_opts, "INT", "min hits for L1 filtering [3]", {'H', "l1-hits"});

2. Line 641: Updated default value

   // Before:
   map_parameters.minimum_hits = 1; // default minimum
   
   // After:
   map_parameters.minimum_hits = 3; // default minimum

Impact

• The L1 filtering will now require at least 3 hits by default (instead of 1)
• This makes the filtering more stringent, reducing spurious mappings
• Users can still override this with -H parameter if needed

Verification

$ ./bin/wfmash --help | grep l1-hits
-H[INT], --l1-hits=[INT]         min hits for L1 filtering [3]

The program now uses 3 as the default minimum hits for L1 filtering.