Merge pull request #251 from paulsengroup/fix/weights

Various improvements to balancing::Weights
paulsengroup · Sep 15, 2024 · 365f138 · 365f138
2 parents f90cadb + 8bbd1ea
commit 365f138
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Showing 40 changed files with 1,648 additions and 385 deletions.
diff --git a/benchmark/fetch_and_sum/fetch_and_sum.cpp b/benchmark/fetch_and_sum/fetch_and_sum.cpp
@@ -52,7 +52,7 @@ template <typename PixelIt>
 }
 
 void fetch_and_sum(const Config &c, cooler::File &&clr) {
-  auto weights = clr.normalization(c.weights);
+  auto weights = clr.normalization_ptr(c.weights);
 
   std::string line;
   while (std::getline(std::cin, line)) {

diff --git a/src/hictk/balance/balance.cpp b/src/hictk/balance/balance.cpp
@@ -69,7 +69,7 @@ static void write_weights_cooler(std::string_view uri, const BalanceConfig& c,
   }
 
   cooler::Dataset dset(cooler::RootGroup{clr.getGroup(grp)}, path, 0.0);
-  dset.append(weights(weights.type()));
+  dset.append(weights.begin(), weights.end());
 
   dset.write_attribute("cis_only", c.mode == "cis");
   dset.write_attribute("divisive_weights", weights.type() == balancing::Weights::Type::DIVISIVE);

diff --git a/src/hictk/convert/cool_to_hic.cpp b/src/hictk/convert/cool_to_hic.cpp
@@ -52,7 +52,7 @@ static void copy_normalization_vector(hic::internal::HiCFileWriter& w, const coo
   }
 
   try {
-    const auto& weights = *clr.normalization(norm);
+    const auto& weights = clr.normalization(norm);
 
     const auto norm_name = norm.to_string() == "weight" ? "ICE" : norm.to_string();
     SPDLOG_INFO(FMT_STRING("[{}] adding {} normalization vector"), resolution, norm_name);

diff --git a/src/libhictk/balancing/include/hictk/balancing/impl/scale_impl.hpp b/src/libhictk/balancing/include/hictk/balancing/impl/scale_impl.hpp
@@ -57,7 +57,7 @@ inline SCALE::SCALE(const File& f, Type type, const Params& params) {
 
 template <typename PixelIt>
 inline SCALE::SCALE(PixelIt first, PixelIt last, const hictk::BinTable& bins, const Params& params)
-    : _biases(VC{first, last, bins}.get_weights()(balancing::Weights::Type::DIVISIVE)),
+    : _biases(VC{first, last, bins}.get_weights().to_vector(balancing::Weights::Type::DIVISIVE)),
       _convergence_stats(ConvergenceStats{false, false, 1000, 0, 10.0 * (1.0 + params.tol)}),
       _tpool(params.threads > 1 ? std::make_unique<BS::thread_pool>(params.threads) : nullptr) {
   if (bins.type() == BinTable::Type::variable) {
@@ -268,7 +268,7 @@ inline auto SCALE::compute_trans(const File& f, const Params& params) -> Result
 
   return {{0, f.bins().size()},
           scale.get_scale(),
-          scale.get_weights(false)(balancing::Weights::Type::DIVISIVE)};
+          scale.get_weights(false).to_vector(balancing::Weights::Type::DIVISIVE)};
 }
 
 template <typename File>
@@ -278,7 +278,7 @@ inline auto SCALE::compute_gw(const File& f, const Params& params) -> Result {
 
   return {{0, f.bins().size()},
           scale.get_scale(),
-          scale.get_weights(false)(balancing::Weights::Type::DIVISIVE)};
+          scale.get_weights(false).to_vector(balancing::Weights::Type::DIVISIVE)};
 }
 
 template <typename Matrix>

diff --git a/src/libhictk/balancing/include/hictk/balancing/impl/vc_impl.hpp b/src/libhictk/balancing/include/hictk/balancing/impl/vc_impl.hpp
@@ -157,7 +157,7 @@ inline auto VC::compute_trans(const File& f) -> Result {
 
   return {{0, f.bins().size()},
           vc.get_scale(),
-          vc.get_weights(false)(balancing::Weights::Type::DIVISIVE)};
+          vc.get_weights(false).to_vector(balancing::Weights::Type::DIVISIVE)};
 }
 
 template <typename File>
@@ -167,7 +167,7 @@ inline auto VC::compute_gw(const File& f) -> Result {
 
   return {{0, f.bins().size()},
           vc.get_scale(),
-          vc.get_weights(false)(balancing::Weights::Type::DIVISIVE)};
+          vc.get_weights(false).to_vector(balancing::Weights::Type::DIVISIVE)};
 }
 
 }  // namespace hictk::balancing