fix comments and propagate adam's change

src/alignment.cpp

@@ -1798,7 +1798,7 @@ void normalize_alignment(Alignment& alignment) {
     if (doing_normalization) {
         // we found things we needed to normalize away, so we must have built the normalized
         // path, now replace the original with it
-        *alignment.mutable_path() = move(normalized);
+        *alignment.mutable_path() = std::move(normalized);
     }
 }
 

src/alignment.hpp

@@ -297,8 +297,8 @@ map<id_t, int> alignment_quality_per_node(const Alignment& aln);
 /// Parse regions from the given BED file into Alignments in a vector.
 /// Reads the optional name, is_reverse, and score fields if present, and populates the relevant Alignment fields.
 /// Skips and warns about malformed or illegal BED records.
+/// If the optional AlignmentEmitter argument is provided, emit the alignments (and flush the vector once in a while).
 void parse_bed_regions(istream& bedstream, const PathPositionHandleGraph* graph, vector<Alignment>* out_alignments, vg::io::AlignmentEmitter* aln_emitter = nullptr);
-// void parse_bed_regions(istream& bedstream, const PathPositionHandleGraph* graph, vector<Alignment>* out_alignments);
 void parse_gff_regions(istream& gtfstream, const PathPositionHandleGraph* graph, vector<Alignment>* out_alignments, vg::io::AlignmentEmitter* aln_emitter = nullptr);
 
 Position alignment_start(const Alignment& aln);

src/subcommand/annotate_main.cpp

@@ -485,7 +485,6 @@ int main_annotate(int argc, char** argv) {
 
             for (auto& gff_name : gff_names) {
                 get_input_file(gff_name, [&](istream& gff_stream) {
-                    // parse_bed_regions(gff_stream, xg_index, aln_emitter);
                     vector<Alignment> buffer;
                     parse_gff_regions(gff_stream, xg_index, &buffer, alignment_emitter.get());
                 });