Merge pull request #97 from paulsengroup/bug/hic-fetch

Fix bug when fetching trans interactions from .hic files
paulsengroup · Jan 8, 2024 · 446d174 · 446d174
2 parents 51f0aff + f6dd34c
commit 446d174
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp b/src/libhictk/hic/include/hictk/hic/impl/index_impl.hpp
@@ -155,25 +155,26 @@ inline auto Index::generate_block_list(std::size_t bin1, std::size_t bin2, std::
   const auto row1 = bin3 / _block_bin_count;
   const auto row2 = (bin4 + 1) / _block_bin_count;
 
-  std::vector<BlockIndex> buffer{};
+  phmap::flat_hash_set<BlockIndex> buffer{};
   for (auto row = row1; row <= row2; ++row) {
     for (auto col = col1; col <= col2; ++col) {
       const auto block_id = (row * block_column_count()) + col;
       const auto match = _buffer.find(BlockIndex{block_id, 0, 0, _block_column_count});
       if (match != _buffer.end()) {
-        buffer.emplace_back(*match);
+        buffer.emplace(*match);
       }
     }
   }
 
+  std::vector<BlockIndex> flat_buffer(buffer.begin(), buffer.end());
   // Sort first by row, then by column
-  std::sort(buffer.begin(), buffer.end(), [](const BlockIndex &b1, const BlockIndex &b2) {
+  std::sort(flat_buffer.begin(), flat_buffer.end(), [](const BlockIndex &b1, const BlockIndex &b2) {
     if (b1.coords().i1 != b2.coords().i1) {
       return b1.coords().i1 < b2.coords().i1;
     }
     return b1.coords().i2 < b2.coords().i2;
   });
-  return buffer;
+  return flat_buffer;
 }
 
 inline auto Index::generate_block_list_intra_v9plus(std::size_t bin1, std::size_t bin2,

diff --git a/test/units/file/file_test.cpp b/test/units/file/file_test.cpp
@@ -23,7 +23,7 @@ namespace hictk::test::file {
 inline const std::filesystem::path datadir{"test/data"};  // NOLINT(cert-err58-cpp)
 
 // NOLINTNEXTLINE(readability-function-cognitive-complexity)
-TEST_CASE("File", "[file][short]") {
+TEST_CASE("HiC: File", "[file][short]") {
   const std::uint32_t resolution = 1'000'000;
   const auto path_hic = (datadir / "hic" / "4DNFIZ1ZVXC8.hic8").string();
   const auto path_cooler = (datadir / "integration_tests" / "4DNFIZ1ZVXC8.mcool").string();