Refactoring

src/aln.hpp

@@ -55,17 +55,23 @@ struct AlignmentStatistics {
     }
 };
 
-struct mapping_params {
+struct MappingParameters {
     int r { 150 };
     int max_secondary { 0 };
     float dropoff_threshold { 0.5 };
-    int R { 2 };
-    int maxTries { 20 };
+    int rescue_level { 2 };
+    int max_tries { 20 };
     int rescue_cutoff;
     bool is_sam_out { true };
     CigarOps cigar_ops{CigarOps::M};
     bool output_unmapped { true };
     bool details{false};
+
+    void verify() const {
+        if (max_tries < 1) {
+            throw BadParameter("max_tries must be greater than zero");
+        }
+    }
 };
 
 class i_dist_est {
@@ -88,7 +94,7 @@ void align_PE_read(
     AlignmentStatistics& statistics,
     i_dist_est& isize_est,
     const Aligner& aligner,
-    const mapping_params& map_param,
+    const MappingParameters& map_param,
     const IndexParameters& index_parameters,
     const References& references,
     const StrobemerIndex& index
@@ -100,7 +106,7 @@ void align_SE_read(
     std::string& outstring,
     AlignmentStatistics& statistics,
     const Aligner& aligner,
-    const mapping_params& map_param,
+    const MappingParameters& map_param,
     const IndexParameters& index_parameters,
     const References& references,
     const StrobemerIndex& index

src/cmdline.cpp

@@ -122,8 +122,8 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     // Search parameters
     if (f) { opt.f = args::get(f); }
     if (S) { opt.dropoff_threshold = args::get(S); }
-    if (M) { opt.maxTries = args::get(M); }
-    if (R) { opt.R = args::get(R); }
+    if (M) { opt.max_tries = args::get(M); }
+    if (R) { opt.rescue_level = args::get(R); }
 
     // Reference and read files
     opt.ref_filename = args::get(ref_filename);

src/cmdline.hpp

@@ -52,8 +52,8 @@ struct CommandLineOptions {
     // Search parameters
     float f { 0.0002 };
     float dropoff_threshold { 0.5 };
-    int maxTries { 20 };
-    int R { 2 };
+    int max_tries { 20 };
+    int rescue_level { 2 };
 
     // Reference and read files
     std::string ref_filename; // This is either a fasta file or an index file - if fasta, indexing will be run

src/main.cpp

@@ -56,15 +56,15 @@ void warn_if_no_optimizations() {
     }
 }
 
-void log_parameters(const IndexParameters& index_parameters, const mapping_params& map_param, const alignment_params& aln_params) {
+void log_parameters(const IndexParameters& index_parameters, const MappingParameters& map_param, const alignment_params& aln_params) {
     logger.debug() << "Using" << std::endl
         << "k: " << index_parameters.syncmer.k << std::endl
         << "s: " << index_parameters.syncmer.s << std::endl
         << "w_min: " << index_parameters.randstrobe.w_min << std::endl
         << "w_max: " << index_parameters.randstrobe.w_max << std::endl
         << "Read length (r): " << map_param.r << std::endl
         << "Maximum seed length: " << index_parameters.randstrobe.max_dist + index_parameters.syncmer.k << std::endl
-        << "R: " << map_param.R << std::endl
+        << "R: " << map_param.rescue_level << std::endl
         << "Expected [w_min, w_max] in #syncmers: [" << index_parameters.randstrobe.w_min << ", " << index_parameters.randstrobe.w_max << "]" << std::endl
         << "Expected [w_min, w_max] in #nucleotides: [" << (index_parameters.syncmer.k - index_parameters.syncmer.s + 1) * index_parameters.randstrobe.w_min << ", " << (index_parameters.syncmer.k - index_parameters.syncmer.s + 1) * index_parameters.randstrobe.w_max << "]" << std::endl
         << "A: " << aln_params.match << std::endl
@@ -168,16 +168,17 @@ int run_strobealign(int argc, char **argv) {
     aln_params.gap_extend = opt.E;
     aln_params.end_bonus = opt.end_bonus;
 
-    mapping_params map_param;
+    MappingParameters map_param;
     map_param.r = opt.r;
     map_param.max_secondary = opt.max_secondary;
     map_param.dropoff_threshold = opt.dropoff_threshold;
-    map_param.R = opt.R;
-    map_param.maxTries = opt.maxTries;
+    map_param.rescue_level = opt.rescue_level;
+    map_param.max_tries = opt.max_tries;
     map_param.is_sam_out = opt.is_sam_out;
     map_param.cigar_ops = opt.cigar_eqx ? CigarOps::EQX : CigarOps::M;
     map_param.output_unmapped = opt.output_unmapped;
     map_param.details = opt.details;
+    map_param.verify();
 
     log_parameters(index_parameters, map_param, aln_params);
     logger.debug() << "Threads: " << opt.n_threads << std::endl;
@@ -257,7 +258,7 @@ int run_strobealign(int argc, char **argv) {
     // Map/align reads
 
     Timer map_align_timer;
-    map_param.rescue_cutoff = map_param.R < 100 ? map_param.R * index.filter_cutoff : 1000;
+    map_param.rescue_cutoff = map_param.rescue_level < 100 ? map_param.rescue_level * index.filter_cutoff : 1000;
     logger.debug() << "Using rescue cutoff: " << map_param.rescue_cutoff << std::endl;
 
     std::streambuf* buf;
@@ -331,7 +332,7 @@ int main(int argc, char **argv) {
     try {
         return run_strobealign(argc, argv);
     } catch (BadParameter& e) {
-        logger.error() << "A mapping or seeding parameter is invalid: " << e.what() << std::endl;
+        logger.error() << "A parameter is invalid: " << e.what() << std::endl;
     } catch (const std::runtime_error& e) {
         logger.error() << "strobealign: " << e.what() << std::endl;
     }

src/nam.cpp

@@ -3,28 +3,28 @@
 namespace {
 
 struct Hit {
-    int query_s;
-    int query_e;
-    int ref_s;
-    int ref_e;
+    int query_start;
+    int query_end;
+    int ref_start;
+    int ref_end;
     bool is_rc = false;
 };
 
 void add_to_hits_per_ref(
     robin_hood::unordered_map<unsigned int, std::vector<Hit>>& hits_per_ref,
-    int query_s,
-    int query_e,
+    int query_start,
+    int query_end,
     bool is_rc,
     const StrobemerIndex& index,
     size_t position,
     int min_diff
 ) {
     for (const auto hash = index.get_hash(position); index.get_hash(position) == hash; ++position) {
-        int ref_s = index.get_strobe1_position(position);
-        int ref_e = ref_s + index.strobe2_offset(position) + index.k();
-        int diff = std::abs((query_e - query_s) - (ref_e - ref_s));
+        int ref_start = index.get_strobe1_position(position);
+        int ref_end = ref_start + index.strobe2_offset(position) + index.k();
+        int diff = std::abs((query_end - query_start) - (ref_end - ref_start));
         if (diff <= min_diff) {
-            hits_per_ref[index.reference_index(position)].push_back(Hit{query_s, query_e, ref_s, ref_e, is_rc});
+            hits_per_ref[index.reference_index(position)].push_back(Hit{query_start, query_end, ref_start, ref_end, is_rc});
             min_diff = diff;
         }
     }
@@ -41,7 +41,7 @@ std::vector<Nam> merge_hits_into_nams(
         if (sort) {
             std::sort(hits.begin(), hits.end(), [](const Hit& a, const Hit& b) -> bool {
                     // first sort on query starts, then on reference starts
-                    return (a.query_s < b.query_s) || ( (a.query_s == b.query_s) && (a.ref_s < b.ref_s) );
+                    return (a.query_start < b.query_start) || ( (a.query_start == b.query_start) && (a.ref_start < b.ref_start) );
                 }
             );
         }
@@ -53,24 +53,24 @@ std::vector<Nam> merge_hits_into_nams(
             for (auto & o : open_nams) {
 
                 // Extend NAM
-                if (( o.is_rc == h.is_rc) && (o.query_prev_hit_startpos < h.query_s) && (h.query_s <= o.query_e ) && (o.ref_prev_hit_startpos < h.ref_s) && (h.ref_s <= o.ref_e) ){
-                    if ( (h.query_e > o.query_e) && (h.ref_e > o.ref_e) ) {
-                        o.query_e = h.query_e;
-                        o.ref_e = h.ref_e;
+                if (( o.is_rc == h.is_rc) && (o.query_prev_hit_startpos < h.query_start) && (h.query_start <= o.query_end ) && (o.ref_prev_hit_startpos < h.ref_start) && (h.ref_start <= o.ref_end) ){
+                    if ( (h.query_end > o.query_end) && (h.ref_end > o.ref_end) ) {
+                        o.query_end = h.query_end;
+                        o.ref_end = h.ref_end;
 //                        o.previous_query_start = h.query_s;
 //                        o.previous_ref_start = h.ref_s; // keeping track so that we don't . Can be caused by interleaved repeats.
-                        o.query_prev_hit_startpos = h.query_s; // log the last strobemer hit in case of outputting paf
-                        o.ref_prev_hit_startpos = h.ref_s; // log the last strobemer hit in case of outputting paf
+                        o.query_prev_hit_startpos = h.query_start; // log the last strobemer hit in case of outputting paf
+                        o.ref_prev_hit_startpos = h.ref_start; // log the last strobemer hit in case of outputting paf
                         o.n_hits ++;
 //                        o.score += (float)1/ (float)h.count;
                         is_added = true;
                         break;
                     }
-                    else if ((h.query_e <= o.query_e) && (h.ref_e <= o.ref_e)) {
+                    else if ((h.query_end <= o.query_end) && (h.ref_end <= o.ref_end)) {
 //                        o.previous_query_start = h.query_s;
 //                        o.previous_ref_start = h.ref_s; // keeping track so that we don't . Can be caused by interleaved repeats.
-                        o.query_prev_hit_startpos = h.query_s; // log the last strobemer hit in case of outputting paf
-                        o.ref_prev_hit_startpos = h.ref_s; // log the last strobemer hit in case of outputting paf
+                        o.query_prev_hit_startpos = h.query_start; // log the last strobemer hit in case of outputting paf
+                        o.ref_prev_hit_startpos = h.ref_start; // log the last strobemer hit in case of outputting paf
                         o.n_hits ++;
 //                        o.score += (float)1/ (float)h.count;
                         is_added = true;
@@ -84,27 +84,27 @@ std::vector<Nam> merge_hits_into_nams(
                 Nam n;
                 n.nam_id = nam_id_cnt;
                 nam_id_cnt ++;
-                n.query_s = h.query_s;
-                n.query_e = h.query_e;
-                n.ref_s = h.ref_s;
-                n.ref_e = h.ref_e;
+                n.query_start = h.query_start;
+                n.query_end = h.query_end;
+                n.ref_start = h.ref_start;
+                n.ref_end = h.ref_end;
                 n.ref_id = ref_id;
 //                n.previous_query_start = h.query_s;
 //                n.previous_ref_start = h.ref_s;
-                n.query_prev_hit_startpos = h.query_s;
-                n.ref_prev_hit_startpos = h.ref_s;
+                n.query_prev_hit_startpos = h.query_start;
+                n.ref_prev_hit_startpos = h.ref_start;
                 n.n_hits = 1;
                 n.is_rc = h.is_rc;
 //                n.score += (float)1 / (float)h.count;
                 open_nams.push_back(n);
             }
 
             // Only filter if we have advanced at least k nucleotides
-            if (h.query_s > prev_q_start + k) {
+            if (h.query_start > prev_q_start + k) {
 
                 // Output all NAMs from open_matches to final_nams that the current hit have passed
                 for (auto &n : open_nams) {
-                    if (n.query_e < h.query_s) {
+                    if (n.query_end < h.query_start) {
                         int n_max_span = std::max(n.query_span(), n.ref_span());
                         int n_min_span = std::min(n.query_span(), n.ref_span());
                         float n_score;
@@ -116,10 +116,10 @@ std::vector<Nam> merge_hits_into_nams(
                 }
 
                 // Remove all NAMs from open_matches that the current hit have passed
-                auto c = h.query_s;
-                auto predicate = [c](decltype(open_nams)::value_type const &nam) { return nam.query_e < c; };
+                auto c = h.query_start;
+                auto predicate = [c](decltype(open_nams)::value_type const &nam) { return nam.query_end < c; };
                 open_nams.erase(std::remove_if(open_nams.begin(), open_nams.end(), predicate), open_nams.end());
-                prev_q_start = h.query_s;
+                prev_q_start = h.query_start;
             }
         }
 
@@ -180,13 +180,13 @@ std::vector<Nam> find_nams_rescue(
     struct RescueHit {
         unsigned int count;
         size_t position;
-        unsigned int query_s;
-        unsigned int query_e;
+        unsigned int query_start;
+        unsigned int query_end;
         bool is_rc;
 
         bool operator< (const RescueHit& rhs) const {
-            return std::tie(count, query_s, query_e, is_rc)
-                < std::tie(rhs.count, rhs.query_s, rhs.query_e, rhs.is_rc);
+            return std::tie(count, query_start, query_end, is_rc)
+                < std::tie(rhs.count, rhs.query_start, rhs.query_end, rhs.is_rc);
         }
     };
 
@@ -218,7 +218,7 @@ std::vector<Nam> find_nams_rescue(
             if ((rh.count > filter_cutoff && cnt >= 5) || rh.count > 1000) {
                 break;
             }
-            add_to_hits_per_ref(hits_per_ref, rh.query_s, rh.query_e, rh.is_rc, index, rh.position, 1000);
+            add_to_hits_per_ref(hits_per_ref, rh.query_start, rh.query_end, rh.is_rc, index, rh.position, 1000);
             cnt++;
         }
     }
@@ -227,6 +227,6 @@ std::vector<Nam> find_nams_rescue(
 }
 
 std::ostream& operator<<(std::ostream& os, const Nam& n) {
-    os << "Nam(ref_id=" << n.ref_id << ", query: " << n.query_s << ".." << n.query_e << ", ref: " << n.ref_s << ".." << n.ref_e << ", score=" << n.score << ")";
+    os << "Nam(ref_id=" << n.ref_id << ", query: " << n.query_start << ".." << n.query_end << ", ref: " << n.ref_start << ".." << n.ref_end << ", score=" << n.score << ")";
     return os;
 }

src/nam.hpp

@@ -8,11 +8,11 @@
 // Non-overlapping approximate match
 struct Nam {
     int nam_id;
-    int query_s;
-    int query_e;
+    int query_start;
+    int query_end;
     int query_prev_hit_startpos;
-    int ref_s;
-    int ref_e;
+    int ref_start;
+    int ref_end;
     int ref_prev_hit_startpos;
     int n_hits = 0;
     int ref_id;
@@ -22,11 +22,11 @@ struct Nam {
     bool is_rc = false;
 
     int ref_span() const {
-        return ref_e - ref_s;
+        return ref_end - ref_start;
     }
 
     int query_span() const {
-        return query_e - query_s;
+        return query_end - query_start;
     }
 };
 

src/paf.cpp

@@ -15,14 +15,14 @@
  * 12 mapping quality (0-255; 255 for missing)
  */
 void output_hits_paf_PE(std::string &paf_output, const Nam &n, const std::string &query_name, const References& references, int k, int read_len) {
-    if (n.ref_s < 0 ) {
+    if (n.ref_start < 0 ) {
         return;
     }
     paf_output.append(query_name);
     paf_output.append("\t");
     paf_output.append(std::to_string(read_len));
     paf_output.append("\t");
-    paf_output.append(std::to_string(n.query_s));
+    paf_output.append(std::to_string(n.query_start));
     paf_output.append("\t");
     paf_output.append(std::to_string(n.query_prev_hit_startpos + k));
     paf_output.append("\t");
@@ -32,13 +32,13 @@ void output_hits_paf_PE(std::string &paf_output, const Nam &n, const std::string
     paf_output.append("\t");
     paf_output.append(std::to_string(references.lengths[n.ref_id]));
     paf_output.append("\t");
-    paf_output.append(std::to_string(n.ref_s));
+    paf_output.append(std::to_string(n.ref_start));
     paf_output.append("\t");
     paf_output.append(std::to_string(n.ref_prev_hit_startpos + k));
     paf_output.append("\t");
     paf_output.append(std::to_string(n.n_hits));
     paf_output.append("\t");
-    paf_output.append(std::to_string(n.ref_prev_hit_startpos + k - n.ref_s));
+    paf_output.append(std::to_string(n.ref_prev_hit_startpos + k - n.ref_start));
     paf_output.append("\t255\n");
 }
 

src/pc.cpp

@@ -135,7 +135,7 @@ void perform_task(
     AlignmentStatistics& statistics,
     int& done,
     const alignment_params &aln_params,
-    const mapping_params &map_param,
+    const MappingParameters &map_param,
     const IndexParameters& index_parameters,
     const References& references,
     const StrobemerIndex& index,

src/pc.hpp

@@ -64,7 +64,7 @@ class OutputBuffer {
 
 void perform_task(InputBuffer &input_buffer, OutputBuffer &output_buffer,
                   AlignmentStatistics& statistics, int& done, const alignment_params &aln_params,
-                  const mapping_params &map_param, const IndexParameters& index_parameters, const References& references, const StrobemerIndex& index, const std::string& read_group_id);
+                  const MappingParameters &map_param, const IndexParameters& index_parameters, const References& references, const StrobemerIndex& index, const std::string& read_group_id);
 
 bool same_name(const std::string& n1, const std::string& n2);
 

src/python/strobealign.cpp

@@ -144,10 +144,10 @@ NB_MODULE(strobealign_extension, m_) {
     nb::bind_vector<QueryRandstrobeVector>(m, "QueryRandstrobeVector");
 
     nb::class_<Nam>(m, "Nam")
-        .def_ro("query_start", &Nam::query_s)
-        .def_ro("query_end", &Nam::query_e)
-        .def_ro("ref_start", &Nam::ref_s)
-        .def_ro("ref_end", &Nam::ref_e)
+        .def_ro("query_start", &Nam::query_start)
+        .def_ro("query_end", &Nam::query_end)
+        .def_ro("ref_start", &Nam::ref_start)
+        .def_ro("ref_end", &Nam::ref_end)
         .def_ro("score", &Nam::score)
         .def_ro("n_hits", &Nam::n_hits)
         .def_ro("reference_index", &Nam::ref_id)