Keep haplotype phase number when converting to reference path

src/subcommand/convert_main.cpp

@@ -609,16 +609,9 @@ void graph_to_xg_adjusting_paths(const PathHandleGraph* input, xg::XG* output, c
                 // Compose the new reference-ified metadata
                 std::string sample = input->get_sample_name(path);
                 std::string locus = input->get_locus_name(path);
-                int64_t haplotype;
-                if (sample_to_haplotypes[sample].size() > 1) {
-                    // We should preserve the haplotype because we have multiple
-                    // haplotype phases of this sample.
-                    haplotype = input->get_haplotype(path);
-                } else {
-                    // We should drop the haplotype number because this sample has only
-                    // one haplotype phase.
-                    haplotype = PathMetadata::NO_HAPLOTYPE;
-                }
+                // We should always preserve the haplotype phase number; we
+                // will need it if we ever want to go back to haplotype sense.
+                int64_t haplotype = input->get_haplotype(path);
                 auto subrange = input->get_subrange(path);
 
                 // Make a new name with reference-ified metadata.