Make giraffe build long read minimizers for long read presets

vgteam · Nov 25, 2024 · 1c97950 · 1c97950 · adamnovak · Nov 25, 2024
1 parent ae25abf
commit 1c97950
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Showing 2 changed files with 8 additions and 0 deletions.
diff --git a/src/index_registry.cpp b/src/index_registry.cpp
@@ -4080,6 +4080,7 @@ IndexRegistry VGIndexes::get_vg_index_registry() {
                                 const IndexGroup& constructing) {
         if (IndexingParameters::verbosity != IndexingParameters::None) {
             cerr << "[IndexRegistry]: Constructing minimizer index and associated zipcodes." << endl;
+            cerr << "\tuse parameters -k " << IndexingParameters::minimizer_k << " -w " << IndexingParameters::minimizer_w << (IndexingParameters::minimizer_W ? " -W " : "") << endl;
         }
 
         // TODO: should the distance index input be a joint simplification to avoid serializing it?

diff --git a/src/subcommand/giraffe_main.cpp b/src/subcommand/giraffe_main.cpp
@@ -1367,6 +1367,13 @@ int main_giraffe(int argc, char** argv) {
                     } else {
                         // Apply the preset values.
                         found->second.apply(*parser);
+
+                        if (param_preset == "hifi" || param_preset == "r10") {
+                            //Set the minimizer parameters for the index registry to make minimizers for long reads
+                            IndexingParameters::minimizer_k=31;
+                            IndexingParameters::minimizer_w=50;
+                            IndexingParameters::minimizer_W=true;
+                        }
                     }
                 }
                 break;