fix: add missing functions

src/fmindex-collection/utils.h

@@ -170,4 +170,73 @@ auto createSequences_32(Sequences auto const& _input, int samplingRate, bool rev
 }
 
 
+inline auto createSA_32(std::span<uint32_t const> input, size_t threadNbr) -> std::vector<int32_t> {
+    auto sa = std::vector<int32_t>(input.size());
+    if (input.size() == 0) {
+        return sa;
+    }
+#if LIBSAIS_OPENMP
+    auto r = libsais_int_omp((int32_t*)input.data(), sa.data(), input.size(), 0, nullptr, threadNbr);
+#else
+    (void)threadNbr; // Unused if no openmp is available
+    auto r = libsais_int((int32_t*)input.data(), sa.data(), input.size(), 65536, 0);
+#endif
+
+    if (r != 0) { throw std::runtime_error("something went wrong constructing the SA"); }
+    return sa;
+}
+
+
+inline auto createBWT_32(std::span<uint32_t const> input, std::span<int32_t const> sa) -> std::vector<uint32_t> {
+    assert(input.size() == sa.size());
+    auto bwt = std::vector<uint32_t>{};
+    bwt.resize(input.size());
+    for (size_t i{0}; i < sa.size(); ++i) {
+        bwt[i] = input[(sa[i] + input.size() - 1) % input.size()];
+    }
+    return bwt;
+}
+
+auto createSequences_32(Sequences auto const& _input, int samplingRate, bool reverse=false) -> std::tuple<size_t, std::vector<uint32_t>, std::vector<std::tuple<size_t, size_t>>> {
+    // compute total numbers of bytes of the text including delimiters "$"
+    size_t totalSize{};
+    for (auto const& l : _input) {
+        auto textLen    = l.size();
+        auto delimLen = samplingRate - textLen % samplingRate; // Make sure it is always a multiple of samplingRate
+        totalSize += textLen + delimLen;
+    }
+
+    // our concatenated sequences with delimiters
+    auto inputText = std::vector<uint32_t>{};
+    inputText.reserve(totalSize);
+
+    // list of sizes of the individual sequences
+    auto inputSizes = std::vector<std::tuple<size_t, size_t>>{};
+    inputSizes.reserve(_input.size());
+
+
+    for (auto const& l : _input) {
+        auto ls = l.size();
+        // number of delimiters ('$') which need to be added. It must be at least one, and it
+        // has to make sure the text will be a multiple of samplingRate
+        size_t delimCount = samplingRate - (ls % samplingRate);
+        inputText.resize(inputText.size() + ls + delimCount, 0);
+
+        if (not reverse) {
+            std::ranges::copy(l, end(inputText) - ls - delimCount);
+        } else {
+//!TODO hack for clang, broken in clang 15
+#if __clang__
+            auto l2 = std::vector<uint32_t>(l);
+            std::ranges::reverse(l2);
+#else
+            auto l2 = std::views::reverse(l);
+#endif
+            std::ranges::copy(l2, end(inputText) - ls - delimCount);
+        }
+
+        inputSizes.emplace_back(l.size(), delimCount);
+    }
+    return {totalSize, inputText, inputSizes};
+}
 }