From 8d75a95e32e52efc198900d0e0038642d6fcbb57 Mon Sep 17 00:00:00 2001
From: "[AldhairMedico]" <amedico@rockefeller.edu>
Date: Mon, 14 Oct 2024 12:20:36 -0400
Subject: [PATCH] Oct 14, 2024: -p IUPAC and -c working

---
 include/tools.h |  9 +++++++++
 src/tools.cpp   | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 include/tools.h
 create mode 100644 src/tools.cpp

diff --git a/include/tools.h b/include/tools.h
new file mode 100644
index 0000000..1260028
--- /dev/null
+++ b/include/tools.h
@@ -0,0 +1,9 @@
+#ifndef TOOLS_H
+#define TOOLS_H
+
+#include <vector>
+#include <string>
+
+void generate_combinations(const std::string &pattern, std::string &current, size_t index, std::vector<std::string> &combinations);
+
+#endif // TOOLS_H
diff --git a/src/tools.cpp b/src/tools.cpp
new file mode 100644
index 0000000..8dfec88
--- /dev/null
+++ b/src/tools.cpp
@@ -0,0 +1,36 @@
+#include "tools.h"
+#include <unordered_map>
+
+std::unordered_map<char, std::vector<char>> IUPAC_DNA_map = {
+    {'A', {'A'}},
+    {'C', {'C'}},
+    {'G', {'G'}},
+    {'T', {'T'}},
+    {'R', {'A', 'G'}},
+    {'Y', {'C', 'T'}},
+    {'M', {'A', 'C'}},
+    {'K', {'G', 'T'}},
+    {'S', {'C', 'G'}},
+    {'W', {'A', 'T'}},
+    {'H', {'A', 'C', 'T'}},
+    {'B', {'C', 'G', 'T'}},
+    {'V', {'A', 'C', 'G'}},
+    {'D', {'A', 'G', 'T'}},
+    {'N', {'A', 'C', 'G', 'T'}}
+};
+
+
+void generate_combinations(const std::string &pattern, std::string &current, size_t index, std::vector<std::string> &combinations) {
+    if (index == pattern.size()) {
+        combinations.push_back(current);
+        return;
+    }
+
+    char base = pattern[index];
+    for (char c : IUPAC_DNA_map[base]) {
+        current[index] = c;
+        generate_combinations(pattern, current, index + 1, combinations);
+    }
+}
+
+