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Expose .hic file attributes #115

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merged 1 commit into from
Feb 11, 2024
Merged

Expose .hic file attributes #115

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1 change: 1 addition & 0 deletions src/libhictk/hic/include/hictk/hic.hpp
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Expand Up @@ -59,6 +59,7 @@ class File {
[[nodiscard]] std::uint64_t nbins() const;
[[nodiscard]] std::uint64_t nchroms() const;
[[nodiscard]] const std::string &assembly() const noexcept;
[[nodiscard]] const phmap::flat_hash_map<std::string, std::string> &attributes() const noexcept;
[[nodiscard]] const std::vector<std::uint32_t> &avail_resolutions() const noexcept;
[[nodiscard]] bool has_normalization(std::string_view normalization) const;
[[nodiscard]] std::vector<balancing::Method> avail_normalizations() const;
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4 changes: 4 additions & 0 deletions src/libhictk/hic/include/hictk/hic/impl/hic_file_impl.hpp
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Expand Up @@ -94,6 +94,10 @@ inline const Reference& File::chromosomes() const noexcept { return bins().chrom

inline const std::string& File::assembly() const noexcept { return _fs->header().genomeID; }

inline const phmap::flat_hash_map<std::string, std::string>& File::attributes() const noexcept {
return _fs->header().attributes;
}

inline const std::vector<std::uint32_t>& File::avail_resolutions() const noexcept {
return _fs->header().resolutions;
}
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1 change: 1 addition & 0 deletions test/units/hic/hic_file_test.cpp
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Expand Up @@ -39,6 +39,7 @@ TEST_CASE("HiC: file accessors", "[hic][short]") {
CHECK(f.version() == 8);
CHECK(f.chromosomes().size() == 9);
CHECK(f.assembly() == "dm6");
CHECK(f.attributes().at("software") == "Juicer Tools Version 1.22.01");

CHECK(f.avail_resolutions().size() == 10);
CHECK(f.avail_resolutions().front() == 1'000);
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