Add a --mcs command-line option for enabling multi-context seeds

ksahlin · Oct 3, 2024 · aef5cd9 · aef5cd9
1 parent c0e9423
commit aef5cd9
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Showing 3 changed files with 5 additions and 1 deletion.
diff --git a/src/cmdline.cpp b/src/cmdline.cpp
@@ -54,6 +54,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     args::ValueFlag<int> end_bonus(parser, "INT", "Soft clipping penalty [10]", {'L'});
 
     args::Group search(parser, "Search parameters:");
+    args::Flag mcs(parser, "mcs", "Use multi-context seeds for finding hits", {"mcs"});
     args::ValueFlag<float> f(parser, "FLOAT", "Top fraction of repetitive strobemers to filter out from sampling [0.0002]", {'f'});
     args::ValueFlag<float> S(parser, "FLOAT", "Try candidate sites with mapping score at least S of maximum mapping score [0.5]", {'S'});
     args::ValueFlag<int> M(parser, "INT", "Maximum number of mapping sites to try [20]", {'M'});
@@ -130,6 +131,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     if (end_bonus) { opt.end_bonus = args::get(end_bonus); }
 
     // Search parameters
+    if (mcs) { opt.mcs = args::get(mcs); }
     if (f) { opt.f = args::get(f); }
     if (S) { opt.dropoff_threshold = args::get(S); }
     if (M) { opt.max_tries = args::get(M); }

diff --git a/src/cmdline.hpp b/src/cmdline.hpp
@@ -62,6 +62,7 @@ struct CommandLineOptions {
     int end_bonus { 10 };
 
     // Search parameters
+    bool mcs { false };
     float f { 0.0002 };
     float dropoff_threshold { 0.5 };
     int max_tries { 20 };

diff --git a/src/main.cpp b/src/main.cpp
@@ -196,7 +196,7 @@ int run_strobealign(int argc, char **argv) {
     map_param.dropoff_threshold = opt.dropoff_threshold;
     map_param.rescue_level = opt.rescue_level;
     map_param.max_tries = opt.max_tries;
-    map_param.use_mcs = false; //opt.r < 200;
+    map_param.use_mcs = opt.mcs;
     map_param.output_format = (
             opt.is_abundance_out ? OutputFormat::Abundance :
             opt.is_sam_out ? OutputFormat::SAM :
@@ -231,6 +231,7 @@ int run_strobealign(int argc, char **argv) {
     }
 
     logger.debug() << "Auxiliary hash length: " << index_parameters.randstrobe.aux_len << "\n";
+    logger.info() << "Using multi-context seeds: " << (map_param.use_mcs ? "yes" : "no") << '\n';
     StrobemerIndex index(references, index_parameters, opt.bits);
     if (opt.use_index) {
         // Read the index from a file