From 4a624fe5f0faab6451dade056bf74e04d7d710dc Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Sun, 24 Sep 2023 13:28:44 +0200
Subject: [PATCH] Bugfix

---
 .../balancing/include/hictk/balancing/ice.hpp |  2 +-
 .../include/hictk/balancing/impl/ice_impl.hpp | 20 ++++++-------------
 .../include/hictk/balancing/sparse_matrix.hpp |  4 ++--
 .../cooler/include/hictk/cooler/cooler.hpp    | 10 ++++------
 4 files changed, 13 insertions(+), 23 deletions(-)

diff --git a/src/libhictk/balancing/include/hictk/balancing/ice.hpp b/src/libhictk/balancing/include/hictk/balancing/ice.hpp
index ce08b580..4c05d2f1 100644
--- a/src/libhictk/balancing/include/hictk/balancing/ice.hpp
+++ b/src/libhictk/balancing/include/hictk/balancing/ice.hpp
@@ -14,7 +14,7 @@
 namespace hictk::balancing {
 
 class ICE {
-  std::vector<std::size_t> _chrom_offsets{};
+  std::vector<std::uint64_t> _chrom_offsets{};
   std::vector<double> _biases{};
   std::vector<double> _variance{};
   std::vector<double> _scale{};
diff --git a/src/libhictk/balancing/include/hictk/balancing/impl/ice_impl.hpp b/src/libhictk/balancing/include/hictk/balancing/impl/ice_impl.hpp
index ff806751..4a29cb79 100644
--- a/src/libhictk/balancing/include/hictk/balancing/impl/ice_impl.hpp
+++ b/src/libhictk/balancing/include/hictk/balancing/impl/ice_impl.hpp
@@ -145,14 +145,10 @@ inline void ICE::balance_cis(const MatrixT& matrix, const BinTable& bins, std::s
 template <typename File>
 auto ICE::construct_sparse_matrix(const File& f, Type type, std::size_t num_masked_diags)
     -> SparseMatrix {
-  switch (type) {
-    case Type::cis:
-      return construct_sparse_matrix_cis(f, num_masked_diags);
-    case Type::trans:
-      [[fallthrough]];
-    case Type::gw:
-      return construct_sparse_matrix_gw(f, num_masked_diags);
+  if (type == Type::cis) {
+    return construct_sparse_matrix_cis(f, num_masked_diags);
   }
+  return construct_sparse_matrix_gw(f, num_masked_diags);
 }
 
 template <typename File>
@@ -252,14 +248,10 @@ template <typename File>
 auto ICE::construct_sparse_matrix_chunked(const File& f, Type type, std::size_t num_masked_diags,
                                           const std::filesystem::path& tmpfile,
                                           std::size_t chunk_size) -> SparseMatrixChunked {
-  switch (type) {
-    case Type::cis:
-      return construct_sparse_matrix_chunked_cis(f, num_masked_diags, tmpfile, chunk_size);
-    case Type::trans:
-      [[fallthrough]];
-    case Type::gw:
-      return construct_sparse_matrix_chunked_gw(f, num_masked_diags, tmpfile, chunk_size);
+  if (type == Type::cis) {
+    return construct_sparse_matrix_chunked_cis(f, num_masked_diags, tmpfile, chunk_size);
   }
+  return construct_sparse_matrix_chunked_gw(f, num_masked_diags, tmpfile, chunk_size);
 }
 
 template <typename File>
diff --git a/src/libhictk/balancing/include/hictk/balancing/sparse_matrix.hpp b/src/libhictk/balancing/include/hictk/balancing/sparse_matrix.hpp
index b5b21b21..4bcecf3e 100644
--- a/src/libhictk/balancing/include/hictk/balancing/sparse_matrix.hpp
+++ b/src/libhictk/balancing/include/hictk/balancing/sparse_matrix.hpp
@@ -21,8 +21,8 @@ class SparseMatrix {
   std::vector<double> _counts{};
 
   std::uint32_t _chrom_id{};  // ID of the chromosome that is being procesed
-  std::vector<std::size_t> _chrom_offsets{};
-  std::vector<std::size_t> _bin1_offsets{};
+  std::vector<std::uint64_t> _chrom_offsets{};
+  std::vector<std::uint64_t> _bin1_offsets{};
   mutable std::vector<double> _marg{};
 
   static constexpr auto _gw_id = std::numeric_limits<std::uint32_t>::max();
diff --git a/src/libhictk/cooler/include/hictk/cooler/cooler.hpp b/src/libhictk/cooler/include/hictk/cooler/cooler.hpp
index 9737b07a..064a4178 100644
--- a/src/libhictk/cooler/include/hictk/cooler/cooler.hpp
+++ b/src/libhictk/cooler/include/hictk/cooler/cooler.hpp
@@ -118,12 +118,10 @@ class File {
   File(File &&other) noexcept(noexcept_move_ctor()) = default;  // NOLINT
 
   // Simple constructor. Open file in read-only mode. Automatically detects pixel count type
-  [[nodiscard]] explicit File(std::string_view uri,
-                              std::size_t cache_size_bytes = DEFAULT_HDF5_CACHE_SIZE,
-                              bool validate = true);
-  [[nodiscard]] explicit File(RootGroup entrypoint,
-                              std::size_t cache_size_bytes = DEFAULT_HDF5_CACHE_SIZE,
-                              bool validate = true);
+  explicit File(std::string_view uri, std::size_t cache_size_bytes = DEFAULT_HDF5_CACHE_SIZE,
+                bool validate = true);
+  explicit File(RootGroup entrypoint, std::size_t cache_size_bytes = DEFAULT_HDF5_CACHE_SIZE,
+                bool validate = true);
 
   [[nodiscard]] static File open_random_access(
       std::string_view uri, std::size_t cache_size_bytes = DEFAULT_HDF5_CACHE_SIZE,