Avoid ODR violations from copy-pasted struct definition.

Interesting that this wasn't picked up in the ~5 years that it was
introduced, but I guess that newer compilers are less cavalier about it.

Author: LTLA

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DropletUtils
-Version: 1.29.3
-Date: 2025-06-13
+Version: 1.29.4
+Date: 2025-07-02
 Title: Utilities for Handling Single-Cell Droplet Data
 Authors@R: c(
     person("Aaron", "Lun", role = "aut"),

src/find_chimeric.cpp

@@ -4,15 +4,6 @@
 #include <vector>
 #include <algorithm>
 
-struct molecule {
-    molecule (size_t i, int u) : index(i), umi(u) {}
-
-    // need to handle situations where one sample has >2e9 UMIs.
-    // otherwise, using ints for memory efficiency.
-    size_t index; 
-    int umi; 
-};
-
 //[[Rcpp::export(rng=false)]]
 Rcpp::List find_chimeric(Rcpp::StringVector cells, Rcpp::IntegerVector umis, 
     Rcpp::IntegerVector reads, double minfrac, bool diagnostics)
@@ -22,6 +13,15 @@ Rcpp::List find_chimeric(Rcpp::StringVector cells, Rcpp::IntegerVector umis,
         throw std::runtime_error("'reads', 'umis', 'cells' should be of the same length");
     }
 
+    struct molecule {
+        molecule (size_t i, int u) : index(i), umi(u) {}
+
+        // need to handle situations where one sample has >2e9 UMIs.
+        // otherwise, using ints for memory efficiency.
+        size_t index; 
+        int umi; 
+    };
+
     std::vector<molecule> ordering;
     ordering.reserve(nmolecules);
     auto uIt=umis.begin();

src/find_swapped.cpp

@@ -31,15 +31,6 @@ void compare_lists(U left, V right) {
     return;
 }
 
-struct molecule {
-    molecule (int s, size_t i, int g, int u) : index(i), sample(s), gene(g), umi(u) {}
-
-    // need to handle situations where one sample has >2e9 UMIs.
-    // otherwise, using ints for memory efficiency.
-    size_t index; 
-    int sample, gene, umi; 
-};
-
 /* Identifies which molecules should be retained in which samples,
  * given the cell, gene and UMI combination for each molecule per sample.
  * Also returns a diagnostic matrix of molecule-sample read counts.
@@ -56,6 +47,15 @@ Rcpp::List find_swapped(Rcpp::List cells, Rcpp::List genes, Rcpp::List umis, Rcp
     compare_lists(Cells, Umis);
     compare_lists(Cells, Reads);
 
+    struct molecule {
+        molecule (int s, size_t i, int g, int u) : index(i), sample(s), gene(g), umi(u) {}
+
+        // need to handle situations where one sample has >2e9 UMIs.
+        // otherwise, using ints for memory efficiency.
+        size_t index; 
+        int sample, gene, umi; 
+    };
+
     // Setting up the ordering vector.
     const size_t nsamples=Cells.size();
     size_t nmolecules=0;