Struct HiCReader 

pub struct HiCReader { /* private fields */ }

Implementations

impl HiCReader

pub fn open( path: &str, parallel: i64, block_size: Option<u64>, max_blocks: Option<usize>, ) -> Result<Self>

pub fn header(&self) -> &HiCHeader

pub fn footer(&self) -> &HiCFooter

pub fn chr_sizes(&self) -> &ChrMap

pub fn normalizations(&self) -> &[String]

pub fn units(&self) -> &[String]

pub fn bin_sizes(&self, unit: Unit) -> &[i64]

The resolutions the file was built at, for one unit, in file order.

Left in the order the header lists them — largest first, as a hic file writes them — rather than sorted, because a caller indexing this by position would otherwise get a different resolution than the file’s own order gives.

pub fn path(&self) -> &str

pub fn is_closed(&self) -> bool

pub fn parallel(&self) -> usize

pub fn close(&mut self)

pub fn parse_loc(&self, req: &HiCRequest) -> Result<Loc2D>

Resolve a request’s two windows against the file’s own resolutions.

The coordinates go through Locs before parse_loc2d. The two checks are not the same one: Locs demands one start and one end per chromosome id, while parse_loc2d accepts one or two of each and duplicates a single value across both axes. Without the first, two chromosomes and one start read the same window twice instead of being refused.

pub fn read_values(&self, req: &HiCRequest) -> Result<Array2<f32>>

Dense (loc1 bins, loc2 bins).

A bin holding a contact the file cannot value — one the chosen normalization has no factor for, or an expected value of zero — comes back NaN, which is a different answer from def_value, meaning “not observed at all”. This matches straw and hictk.

An out-of-range window pads with def_value like bbi; only the block enumeration is clamped.

pub fn read_sparse_values(&self, req: &HiCRequest) -> Result<CooMatrix>

The same, sparse.

No def_value: a cell this does not list is one no contact reached, which is what a sparse matrix says by leaving it out.

Trait Implementations

impl Debug for HiCReader

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.