From a7a23cb453d3f144f7f20cb114e4b7c312135e09 Mon Sep 17 00:00:00 2001
From: Roberto Rossini <71787608+robomics@users.noreply.github.com>
Date: Thu, 7 Nov 2024 19:37:42 +0100
Subject: [PATCH] Remove dead code

---
 src/libnchg/include/nchg/nchg.hpp |  3 ---
 src/libnchg/nchg.cpp              | 28 -------------------------
 src/nchg/filter/filter.cpp        | 35 -------------------------------
 3 files changed, 66 deletions(-)

diff --git a/src/libnchg/include/nchg/nchg.hpp b/src/libnchg/include/nchg/nchg.hpp
index f58fe55..6b1422b 100644
--- a/src/libnchg/include/nchg/nchg.hpp
+++ b/src/libnchg/include/nchg/nchg.hpp
@@ -111,9 +111,6 @@ class NCHG {
   [[nodiscard]] auto end(const hictk::Chromosome& chrom1, const hictk::Chromosome& chrom2) const
       -> IteratorVariant;
 
-  [[nodiscard]] std::pair<std::vector<double>, phmap::btree_map<hictk::Chromosome, double>>
-  compute_expected_profile() const;
-
  private:
   [[nodiscard]] static std::shared_ptr<const ExpectedMatrixStats> init_exp_matrix(
       const hictk::Chromosome& chrom1, const hictk::Chromosome& chrom2, const hictk::File& f,
diff --git a/src/libnchg/nchg.cpp b/src/libnchg/nchg.cpp
index e26ba9a..a62bd31 100644
--- a/src/libnchg/nchg.cpp
+++ b/src/libnchg/nchg.cpp
@@ -266,32 +266,4 @@ double NCHG::compute_pvalue_nchg(std::vector<double> &buffer, std::uint64_t obs,
   return pvalue < 0 ? 1.0 : pvalue;
 }
 
-std::pair<std::vector<double>, phmap::btree_map<hictk::Chromosome, double>>
-NCHG::compute_expected_profile() const {
-  SPDLOG_INFO("initializing expected matrix weights from genome-wide interactions...");
-
-  return std::visit(
-      [&](const auto &f)
-          -> std::pair<std::vector<double>, phmap::btree_map<hictk::Chromosome, double>> {
-        const auto [selectors, merger] = ExpectedValues::init_pixel_merger_cis(f);
-        if (merger.begin() == merger.end()) [[unlikely]] {
-          phmap::btree_map<hictk::Chromosome, double> scaling_factors{};
-          std::ranges::transform(
-              f.chromosomes(), std::inserter(scaling_factors, scaling_factors.end()),
-              [](const hictk::Chromosome &chrom) { return std::make_pair(chrom, 1.0); });
-          for (const auto &chrom : f.chromosomes()) {
-            scaling_factors.emplace(chrom, 1.0);
-          }
-          return {std::vector<double>(f.bins().size(), 0), scaling_factors};
-        }
-
-        const hictk::transformers::JoinGenomicCoords mjsel(merger.begin(), merger.end(),
-                                                           f.bins_ptr());
-
-        return ExpectedMatrixStats::build_expected_vector(mjsel, f.bins(), params().min_delta,
-                                                          params().max_delta);
-      },
-      _fp->get());
-}
-
 }  // namespace nchg
diff --git a/src/nchg/filter/filter.cpp b/src/nchg/filter/filter.cpp
index bd416ba..0946ca3 100644
--- a/src/nchg/filter/filter.cpp
+++ b/src/nchg/filter/filter.cpp
@@ -30,7 +30,6 @@
 #include <future>
 #include <hictk/chromosome.hpp>
 #include <hictk/numeric_utils.hpp>
-#include <memory>
 #include <numeric>
 #include <ranges>
 #include <set>
@@ -47,40 +46,6 @@
 
 namespace nchg {
 
-struct SharedPtrStringCmp {
-  using is_transparent = void;
-  constexpr bool operator()(const std::shared_ptr<std::string>& a,
-                            const std::shared_ptr<std::string>& b) const noexcept {
-    assert(!!a);
-    assert(!!b);
-    return *a < *b;
-  }
-
-  constexpr bool operator()(const std::string& a,
-                            const std::shared_ptr<std::string>& b) const noexcept {
-    assert(!!b);
-    return a < *b;
-  }
-
-  constexpr bool operator()(const std::shared_ptr<std::string>& a,
-                            const std::string& b) const noexcept {
-    assert(!!a);
-    return *a < b;
-  }
-
-  constexpr bool operator()(std::string_view a,
-                            const std::shared_ptr<std::string>& b) const noexcept {
-    assert(!!b);
-    return a < *b;
-  }
-
-  constexpr bool operator()(const std::shared_ptr<std::string>& a,
-                            std::string_view b) const noexcept {
-    assert(!!a);
-    return *a < b;
-  }
-};
-
 struct StringPairCmp {
   using is_transparent = void;
   constexpr bool operator()(const std::pair<std::string, std::string>& a,