(Polishing) tweak

include/Build_Params.hpp

@@ -34,7 +34,7 @@ class Build_Params
     const std::string output_file_path_;    // Path to the output file.
     const std::optional<cuttlefish::Output_Format> output_format_;  // Output format (0: FASTA, 1: GFAv1, 2: GFAv2, 3: GFA-reduced).
     const bool track_short_seqs_;   // Whether to track input sequences shorter than `k` bases.
-    const bool poly_n_stretch_;   // Whether to include tiles in GFA-reduced output that track the polyN stretches in the input.
+    const bool poly_n_stretch_; // Whether to include tiles in GFA-reduced output that track the polyN stretches in the input.
     const std::string working_dir_path_;    // Path to the working directory (for temporary files).
     const bool path_cover_; // Whether to extract a maximal path cover of the de Bruijn graph.
     const bool save_mph_;   // Option to save the MPH over the vertex set of the de Bruijn graph.

include/Oriented_Unitig.hpp

@@ -25,8 +25,8 @@ class Oriented_Unitig
 
     uint64_t unitig_id;
     cuttlefish::dir_t dir;
-    size_t start_kmer_idx; // Position, on the ref, of the last kmer of the unitig occurrence
-    size_t end_kmer_idx;   // Position, on the ref, of the first kmer of the unitig occurrence
+    size_t start_kmer_idx;  // Position, on the ref, of the last k-mer of the unitig occurrence
+    size_t end_kmer_idx;    // Position, on the ref, of the first k-mer of the unitig occurrence
 
     constexpr static uint64_t INVALID_ID = std::numeric_limits<uint64_t>::max();
 

src/CdBG_GFA_Reduced_Writer.cpp

@@ -80,9 +80,8 @@ void CdBG<k>::write_sequence_tiling(Job_Queue<std::string, Oriented_Unitig>& job
         // Write the path members.
         output << "\t";
 
-        if(poly_n_stretch and left_unitig.start_kmer_idx > 0) {
+        if(poly_n_stretch && left_unitig.start_kmer_idx > 0)
             output << "N" << left_unitig.start_kmer_idx << " ";
-        }
 
         // The first vertex of the path (not inferrable from the path output files).
         output << left_unitig.unitig_id << (left_unitig.dir == cuttlefish::FWD ? "+" : "-");

src/CdBG_GFA_Writer.cpp

@@ -601,24 +601,25 @@ void CdBG<k>::append_edge_to_path(const uint16_t thread_id, const Oriented_Uniti
     // The destination vertex (unitig) is written for each edge.
     // Note that, the very first vertex of the path tiling for the sequence is thus missing in the path outputs.
 
-    (void)left_unitig;
-
     std::string& buffer = path_buffer[thread_id];
     const bool poly_n_stretch = params.poly_n_stretch();
-    const int64_t pk = static_cast<int64_t>(params.k());
 
     // Encode polyN stretch
     // *.{first, last}_kmer_index stores the position of the kmer on the ref.
-    if( poly_n_stretch and ((left_unitig.end_kmer_idx + 1) != right_unitig.start_kmer_idx)) {
+    if(poly_n_stretch && ((left_unitig.end_kmer_idx + 1) != right_unitig.start_kmer_idx))
+    {
         const int64_t nuc_gap = static_cast<int64_t>(right_unitig.start_kmer_idx) - static_cast<int64_t>(left_unitig.end_kmer_idx);
+
         // If left_unitig starts at offset 0 and ends at offset k - 1, the smallest polyN stretch of len 1 starts
-        // with index k, and right unitig must start at k+1.
-        if ( nuc_gap < (pk + 1)) {
+        // with index k, and right unitig must start at k + 1.
+        if(nuc_gap < (k + 1))
+        {
             // Any difference in idxs < k+1 must be invalid.
-            std::cerr << "ERROR: invalid polyN gap length\n";
+            std::cerr << "ERROR: invalid polyN gap length.\n";
             std::exit(EXIT_FAILURE);
         }
-        size_t polyn_gap = static_cast<size_t>(nuc_gap - pk);
+
+        const size_t polyn_gap = static_cast<size_t>(nuc_gap - k);
         buffer += " ";
         buffer += "N";
         buffer += fmt::format_int(polyn_gap).c_str();