Resolved cherry-picking conflicts.

dorado/alignment/Minimap2Index.cpp

@@ -253,6 +253,10 @@ const mm_mapopt_t& Minimap2Index::mapping_options() const {
     return *m_mapping_options;
 }
 
+mm_mapopt_t& Minimap2Index::mapping_options() {
+    return const_cast<mm_mapopt_t&>(const_cast<const Minimap2Index&>(*this).mapping_options());
+}
+
 const Minimap2Options& Minimap2Index::get_options() const { return m_options; }
 
 }  // namespace dorado::alignment

dorado/alignment/Minimap2Index.h

@@ -46,6 +46,7 @@ class Minimap2Index {
     const mm_idx_t* index() const { return m_index.get(); }
     const mm_idxopt_t& index_options() const;
     const mm_mapopt_t& mapping_options() const;
+    mm_mapopt_t& mapping_options();
 
     HeaderSequenceRecords get_sequence_records_for_header() const;
 

dorado/read_pipeline/ErrorCorrectionMapperNode.cpp

@@ -6,11 +6,9 @@
 #include "alignment/Minimap2Index.h"
 #include "alignment/Minimap2IndexSupportTypes.h"
 #include "alignment/Minimap2Options.h"
-#include "alignment/minimap2_args.h"
-#include "alignment/minimap2_wrappers.h"
 #include "utils/PostCondition.h"
 #include "utils/bam_utils.h"
-#include "utils/thread_naming.h"
+#include "utils/thread_utils.h"
 
 #include <htslib/faidx.h>
 #include <htslib/sam.h>
@@ -258,38 +256,36 @@ ErrorCorrectionMapperNode::ErrorCorrectionMapperNode(const std::string& index_fi
           m_index_file(index_file),
           m_num_threads(threads),
           m_reads_queue(5000) {
-    auto options = alignment::create_preset_options("ava-ont");
-    auto& index_options = options.index_options->get();
-    index_options.k = 25;
-    index_options.w = 17;
-    index_options.batch_size = index_size;
-    auto& mapping_options = options.mapping_options->get();
-    mapping_options.bw = 150;
-    mapping_options.bw_long = 2000;
-    mapping_options.min_chain_score = 4000;
-    mapping_options.zdrop = 200;
-    mapping_options.zdrop_inv = 200;
-    mapping_options.occ_dist = 200;
-    mapping_options.flag |= MM_F_EQX;
-
-    // --cs short
-    alignment::mm2::apply_cs_option(options, "short");
+    alignment::Minimap2Options options = alignment::dflt_options;
+    options.kmer_size = 25;
+    options.window_size = 17;
+    options.index_batch_size = index_size;
+    options.mm2_preset = "ava-ont";
+    options.bandwidth = 150;
+    options.bandwidth_long = 2000;
+    options.min_chain_score = 4000;
+    options.zdrop = options.zdrop_inv = 200;
+    options.occ_dist = 200;
+    options.cs = "short";
+    options.dual = "yes";
+    options.cap_kalloc = std::nullopt;
+    options.max_sw_mat = std::nullopt;
 
-    // --dual yes
-    alignment::mm2::apply_dual_option(options, "yes");
+    m_index = std::make_shared<alignment::Minimap2Index>();
+    if (!m_index->initialise(options)) {
+        throw std::runtime_error("Failed to initialize with options.");
+    } else {
+        spdlog::debug("Initialized index options.");
+    }
 
     // reset to larger minimap2 defaults
+    mm_mapopt_t& mapping_options = m_index->mapping_options();
     mm_mapopt_t minimap_default_mapopt;
     mm_mapopt_init(&minimap_default_mapopt);
     mapping_options.cap_kalloc = minimap_default_mapopt.cap_kalloc;
     mapping_options.max_sw_mat = minimap_default_mapopt.max_sw_mat;
+    mapping_options.flag |= MM_F_EQX;
 
-    m_index = std::make_shared<alignment::Minimap2Index>();
-    if (!m_index->initialise(options)) {
-        throw std::runtime_error("Failed to initialize with options.");
-    } else {
-        spdlog::debug("Initialized index options.");
-    }
     spdlog::debug("Loading index...");
     if (m_index->load(index_file, threads, true) != alignment::IndexLoadResult::success) {
         throw std::runtime_error("Failed to load index file " + index_file);