Index H H hictk::Bin (C++ class) hictk::Bin::Bin (C++ function), [1], [2], [3], [4] hictk::Bin::chrom (C++ function) hictk::Bin::end (C++ function) hictk::Bin::has_null_id (C++ function) hictk::Bin::id (C++ function) hictk::Bin::interval (C++ function) hictk::Bin::operator bool (C++ function) hictk::Bin::operator!= (C++ function) hictk::Bin::operator< (C++ function) hictk::Bin::operator<= (C++ function) hictk::Bin::operator== (C++ function) hictk::Bin::operator> (C++ function) hictk::Bin::operator>= (C++ function) hictk::Bin::rel_id (C++ function) hictk::Bin::start (C++ function) hictk::BinTable (C++ class) hictk::BinTable::at (C++ function), [1], [2], [3], [4] hictk::BinTable::at_hint (C++ function) hictk::BinTable::begin (C++ function) hictk::BinTable::BinTable (C++ function), [1], [2], [3] hictk::BinTable::cbegin (C++ function) hictk::BinTable::cend (C++ function) hictk::BinTable::chromosomes (C++ function) hictk::BinTable::concretize (C++ function) hictk::BinTable::empty (C++ function) hictk::BinTable::end (C++ function) hictk::BinTable::find_overlap (C++ function), [1], [2], [3] hictk::BinTable::map_to_bin_id (C++ function), [1], [2] hictk::BinTable::map_to_bin_ids (C++ function) hictk::BinTable::num_bin_prefix_sum (C++ function) hictk::BinTable::num_chromosomes (C++ function) hictk::BinTable::operator!= (C++ function) hictk::BinTable::operator== (C++ function) hictk::BinTable::resolution (C++ function) hictk::BinTable::size (C++ function) hictk::BinTable::subset (C++ function), [1], [2] hictk::Chromosome (C++ class) hictk::Chromosome::Chromosome (C++ function), [1] hictk::Chromosome::id (C++ function) hictk::Chromosome::is_all (C++ function) hictk::Chromosome::name (C++ function) hictk::Chromosome::operator bool (C++ function) hictk::Chromosome::operator!= (C++ function), [1], [2], [3], [4] hictk::Chromosome::operator< (C++ function), [1], [2] hictk::Chromosome::operator<= (C++ function), [1], [2] hictk::Chromosome::operator== (C++ function), [1], [2], [3], [4] hictk::Chromosome::operator> (C++ function), [1], [2] hictk::Chromosome::operator>= (C++ function), [1], [2] hictk::Chromosome::size (C++ function) hictk::cooler::File (C++ class) hictk::cooler::File::append_pixels (C++ function) hictk::cooler::File::attributes (C++ function) hictk::cooler::File::avail_normalizations (C++ function) hictk::cooler::File::begin (C++ function) hictk::cooler::File::bins (C++ function) hictk::cooler::File::bins_ptr (C++ function) hictk::cooler::File::cbegin (C++ function) hictk::cooler::File::cend (C++ function) hictk::cooler::File::chromosomes (C++ function) hictk::cooler::File::close (C++ function) hictk::cooler::File::create (C++ function), [1] hictk::cooler::File::dataset (C++ function), [1] hictk::cooler::File::end (C++ function) hictk::cooler::File::fetch (C++ function), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] hictk::cooler::File::File (C++ function), [1], [2], [3] hictk::cooler::File::flush (C++ function) hictk::cooler::File::group (C++ function), [1] hictk::cooler::File::has_float_pixels (C++ function) hictk::cooler::File::has_integral_pixels (C++ function) hictk::cooler::File::has_normalization (C++ function), [1] hictk::cooler::File::has_pixel_of_type (C++ function) hictk::cooler::File::has_signed_pixels (C++ function) hictk::cooler::File::has_unsigned_pixels (C++ function) hictk::cooler::File::hdf5_path (C++ function) hictk::cooler::File::nbins (C++ function) hictk::cooler::File::nchroms (C++ function) hictk::cooler::File::nnz (C++ function) hictk::cooler::File::normalization (C++ function), [1], [2] hictk::cooler::File::open_random_access (C++ function), [1] hictk::cooler::File::open_read_once (C++ function), [1] hictk::cooler::File::operator bool (C++ function) hictk::cooler::File::operator= (C++ function), [1] hictk::cooler::File::path (C++ function) hictk::cooler::File::pixel_variant (C++ function) hictk::cooler::File::purge_weights (C++ function) hictk::cooler::File::read_normalization (C++ function) hictk::cooler::File::resolution (C++ function) hictk::cooler::File::uri (C++ function) hictk::cooler::File::validate_bins (C++ function) hictk::cooler::File::write_weights (C++ function), [1] hictk::cooler::MultiResFile (C++ class) hictk::cooler::MultiResFile::attributes (C++ function) hictk::cooler::MultiResFile::chromosomes (C++ function) hictk::cooler::MultiResFile::coarsen (C++ function) hictk::cooler::MultiResFile::compute_base_resolution (C++ function) hictk::cooler::MultiResFile::copy_resolution (C++ function) hictk::cooler::MultiResFile::create (C++ function), [1] hictk::cooler::MultiResFile::create_resolution (C++ function) hictk::cooler::MultiResFile::init_resolution (C++ function) hictk::cooler::MultiResFile::MultiResFile (C++ function) hictk::cooler::MultiResFile::open (C++ function) hictk::cooler::MultiResFile::operator bool (C++ function) hictk::cooler::MultiResFile::path (C++ function) hictk::cooler::MultiResFile::resolutions (C++ function) hictk::cooler::PixelSelector (C++ class) hictk::cooler::PixelSelector::begin (C++ function) hictk::cooler::PixelSelector::bins (C++ function) hictk::cooler::PixelSelector::bins_ptr (C++ function) hictk::cooler::PixelSelector::cbegin (C++ function) hictk::cooler::PixelSelector::cend (C++ function) hictk::cooler::PixelSelector::coord1 (C++ function) hictk::cooler::PixelSelector::coord2 (C++ function) hictk::cooler::PixelSelector::end (C++ function) hictk::cooler::PixelSelector::operator!= (C++ function) hictk::cooler::PixelSelector::operator== (C++ function) hictk::cooler::PixelSelector::read_all (C++ function) hictk::cooler::PixelSelector::read_dense (C++ function) hictk::cooler::PixelSelector::read_sparse (C++ function) hictk::cooler::SingleCellFile (C++ class) hictk::cooler::SingleCellFile::aggregate (C++ function) hictk::cooler::SingleCellFile::attributes (C++ function) hictk::cooler::SingleCellFile::bins (C++ function) hictk::cooler::SingleCellFile::cells (C++ function) hictk::cooler::SingleCellFile::chromosomes (C++ function) hictk::cooler::SingleCellFile::create (C++ function) hictk::cooler::SingleCellFile::create_cell (C++ function) hictk::cooler::SingleCellFile::open (C++ function) hictk::cooler::SingleCellFile::operator bool (C++ function) hictk::cooler::SingleCellFile::path (C++ function) hictk::cooler::SingleCellFile::resolution (C++ function) hictk::cooler::SingleCellFile::SingleCellFile (C++ function) hictk::File (C++ class) hictk::File::avail_normalizations (C++ function) hictk::File::bins (C++ function) hictk::File::bins_ptr (C++ function) hictk::File::chromosomes (C++ function) hictk::File::fetch (C++ function), [1], [2], [3], [4] hictk::File::File (C++ function), [1], [2] hictk::File::get (C++ function), [1], [2], [3] hictk::File::has_normalization (C++ function) hictk::File::is_cooler (C++ function) hictk::File::is_hic (C++ function) hictk::File::nbins (C++ function) hictk::File::nchroms (C++ function) hictk::File::path (C++ function) hictk::File::resolution (C++ function) hictk::File::uri (C++ function) hictk::GenomicInterval (C++ class) hictk::GenomicInterval::chrom (C++ function) hictk::GenomicInterval::end (C++ function) hictk::GenomicInterval::GenomicInterval (C++ function), [1], [2] hictk::GenomicInterval::operator bool (C++ function) hictk::GenomicInterval::operator!= (C++ function) hictk::GenomicInterval::operator< (C++ function) hictk::GenomicInterval::operator<= (C++ function) hictk::GenomicInterval::operator== (C++ function) hictk::GenomicInterval::operator> (C++ function) hictk::GenomicInterval::operator>= (C++ function) hictk::GenomicInterval::parse (C++ function) hictk::GenomicInterval::parse_bed (C++ function) hictk::GenomicInterval::parse_ucsc (C++ function) hictk::GenomicInterval::QUERY_TYPE (C++ enum) hictk::GenomicInterval::QUERY_TYPE::BED (C++ enumerator) hictk::GenomicInterval::QUERY_TYPE::UCSC (C++ enumerator) hictk::GenomicInterval::size (C++ function) hictk::GenomicInterval::start (C++ function) hictk::hic::File (C++ class) hictk::hic::File::assembly (C++ function) hictk::hic::File::avail_normalizations (C++ function) hictk::hic::File::avail_resolutions (C++ function) hictk::hic::File::bins (C++ function) hictk::hic::File::bins_ptr (C++ function) hictk::hic::File::block_cache_hit_rate (C++ function) hictk::hic::File::cache_capacity (C++ function) hictk::hic::File::chromosomes (C++ function) hictk::hic::File::clear_cache (C++ function) hictk::hic::File::fetch (C++ function), [1], [2], [3], [4], [5], [6] hictk::hic::File::File (C++ function) hictk::hic::File::has_normalization (C++ function) hictk::hic::File::has_resolution (C++ function) hictk::hic::File::name (C++ function) hictk::hic::File::nbins (C++ function) hictk::hic::File::nchroms (C++ function) hictk::hic::File::num_cached_footers (C++ function) hictk::hic::File::open (C++ function), [1] hictk::hic::File::optimize_cache_size (C++ function) hictk::hic::File::optimize_cache_size_for_iteration (C++ function) hictk::hic::File::optimize_cache_size_for_random_access (C++ function) hictk::hic::File::path (C++ function) hictk::hic::File::purge_footer_cache (C++ function) hictk::hic::File::reset_cache_stats (C++ function) hictk::hic::File::resolution (C++ function) hictk::hic::File::version (C++ function) hictk::hic::MatrixType (C++ enum) hictk::hic::MatrixType::expected (C++ enumerator) hictk::hic::MatrixType::observed (C++ enumerator) hictk::hic::MatrixType::oe (C++ enumerator) hictk::hic::MatrixUnit (C++ enum) hictk::hic::MatrixUnit::BP (C++ enumerator) hictk::hic::MatrixUnit::FRAG (C++ enumerator) hictk::hic::PixelSelector (C++ class) hictk::hic::PixelSelector::begin (C++ function) hictk::hic::PixelSelector::bins (C++ function) hictk::hic::PixelSelector::cbegin (C++ function) hictk::hic::PixelSelector::cend (C++ function) hictk::hic::PixelSelector::chrom1 (C++ function) hictk::hic::PixelSelector::chrom2 (C++ function) hictk::hic::PixelSelector::clear_cache (C++ function) hictk::hic::PixelSelector::coord1 (C++ function) hictk::hic::PixelSelector::coord2 (C++ function) hictk::hic::PixelSelector::empty (C++ function) hictk::hic::PixelSelector::end (C++ function) hictk::hic::PixelSelector::estimate_optimal_cache_size (C++ function) hictk::hic::PixelSelector::is_inter (C++ function) hictk::hic::PixelSelector::is_intra (C++ function) hictk::hic::PixelSelector::matrix_type (C++ function) hictk::hic::PixelSelector::metadata (C++ function) hictk::hic::PixelSelector::normalization (C++ function) hictk::hic::PixelSelector::operator!= (C++ function) hictk::hic::PixelSelector::operator== (C++ function) hictk::hic::PixelSelector::read_all (C++ function) hictk::hic::PixelSelector::read_dense (C++ function) hictk::hic::PixelSelector::read_sparse (C++ function) hictk::hic::PixelSelector::resolution (C++ function) hictk::hic::PixelSelector::unit (C++ function) hictk::hic::PixelSelector::weights1 (C++ function) hictk::hic::PixelSelector::weights2 (C++ function) hictk::hic::QUERY_TYPE (C++ enum) hictk::hic::QUERY_TYPE::BED (C++ enumerator) hictk::hic::QUERY_TYPE::UCSC (C++ enumerator) hictk::Pixel (C++ class) hictk::Pixel::coords (C++ member) hictk::Pixel::count (C++ member) hictk::Pixel::from_4dn_pairs (C++ function) hictk::Pixel::from_bg2 (C++ function) hictk::Pixel::from_coo (C++ function) hictk::Pixel::from_validpair (C++ function) hictk::Pixel::operator bool (C++ function) hictk::Pixel::operator!= (C++ function) hictk::Pixel::operator< (C++ function) hictk::Pixel::operator<= (C++ function) hictk::Pixel::operator== (C++ function) hictk::Pixel::operator> (C++ function) hictk::Pixel::operator>= (C++ function) hictk::Pixel::Pixel (C++ function), [1], [2], [3], [4], [5], [6], [7], [8] hictk::Pixel::to_thin (C++ function) hictk::PixelCoordinates (C++ class) hictk::PixelCoordinates::bin1 (C++ member) hictk::PixelCoordinates::bin2 (C++ member) hictk::PixelCoordinates::is_intra (C++ function) hictk::PixelCoordinates::operator bool (C++ function) hictk::PixelCoordinates::operator!= (C++ function) hictk::PixelCoordinates::operator< (C++ function) hictk::PixelCoordinates::operator<= (C++ function) hictk::PixelCoordinates::operator== (C++ function) hictk::PixelCoordinates::operator> (C++ function) hictk::PixelCoordinates::operator>= (C++ function) hictk::PixelCoordinates::PixelCoordinates (C++ function), [1], [2], [3] hictk::PixelSelector (C++ class) hictk::PixelSelector::begin (C++ function) hictk::PixelSelector::bins (C++ function) hictk::PixelSelector::cbegin (C++ function) hictk::PixelSelector::cend (C++ function) hictk::PixelSelector::coord1 (C++ function) hictk::PixelSelector::coord2 (C++ function) hictk::PixelSelector::end (C++ function) hictk::PixelSelector::get (C++ function), [1], [2], [3] hictk::PixelSelector::read_all (C++ function) hictk::PixelSelector::read_dense (C++ function) hictk::PixelSelector::read_sparse (C++ function) hictk::QUERY_TYPE (C++ enum) hictk::QUERY_TYPE::BED (C++ enumerator) hictk::QUERY_TYPE::UCSC (C++ enumerator) hictk::Reference (C++ class) hictk::Reference::at (C++ function), [1] hictk::Reference::begin (C++ function) hictk::Reference::cbegin (C++ function) hictk::Reference::cend (C++ function) hictk::Reference::chromosome_with_longest_name (C++ function) hictk::Reference::contains (C++ function), [1], [2] hictk::Reference::empty (C++ function) hictk::Reference::end (C++ function) hictk::Reference::find (C++ function), [1], [2] hictk::Reference::from_chrom_sizes (C++ function) hictk::Reference::get_id (C++ function) hictk::Reference::longest_chromosome (C++ function) hictk::Reference::operator!= (C++ function) hictk::Reference::operator== (C++ function) hictk::Reference::operator[] (C++ function), [1] hictk::Reference::rbegin (C++ function) hictk::Reference::rcbegin (C++ function) hictk::Reference::rcend (C++ function) hictk::Reference::Reference (C++ function), [1], [2], [3] hictk::Reference::rend (C++ function) hictk::Reference::size (C++ function) hictk::ThinPixel (C++ class) hictk::ThinPixel::bin1_id (C++ member) hictk::ThinPixel::bin2_id (C++ member) hictk::ThinPixel::count (C++ member) hictk::ThinPixel::from_coo (C++ function), [1] hictk::ThinPixel::null_id (C++ member) hictk::ThinPixel::operator bool (C++ function) hictk::ThinPixel::operator!= (C++ function) hictk::ThinPixel::operator< (C++ function) hictk::ThinPixel::operator<= (C++ function) hictk::ThinPixel::operator== (C++ function) hictk::ThinPixel::operator> (C++ function) hictk::ThinPixel::operator>= (C++ function)