From aef5cd9e64cc130a064d86f85d81381a11069735 Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Thu, 3 Oct 2024 13:05:07 +0200
Subject: [PATCH] Add a --mcs command-line option for enabling multi-context
 seeds

---
 src/cmdline.cpp | 2 ++
 src/cmdline.hpp | 1 +
 src/main.cpp    | 3 ++-
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cmdline.cpp b/src/cmdline.cpp
index ec5f7e70..a4f2c068 100644
--- 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
index f780ba3d..7cd1e730 100644
--- 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
index 30f5c368..660e1678 100644
--- 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