Struct ChrMap 

pub struct ChrMap { /* private fields */ }

Insertion-ordered chromosome map. Order is the file’s reference order, which callers depend on — chr_sizes is documented as coming back in it, and the case-insensitive walk in try_lookup — private, so not linked — resolves ties by it.

Implementations

impl ChrMap

pub fn from_entries(entries: impl IntoIterator<Item = (String, i64)>) -> Self

Build from names and sizes, numbering them by insertion order.

A name given twice keeps the index it was first given, and its later size wins. Numbering from map.len() instead left the two entries sharing an index — the second overwrote the first in the map while the count stood still — and an index is what a data record carries.

pub fn from_indexed_entries( entries: impl IntoIterator<Item = (String, i64, usize)>, ) -> Self

Build from names, sizes and the indices the file gives them.

A bbi chromosome tree and a BAM reference list both store an explicit index, and that index is what data records and R-tree items carry — so it cannot be re-derived from position here. Entries are sorted by it, which is the order chr_sizes reports them in.

pub fn with_key_size(self, key_size: usize) -> Self

The fixed key width a bbi chromosome tree declares. Message-only.

pub fn declared_key_size(&self) -> Option<usize>

pub fn len(&self) -> usize

pub fn is_empty(&self) -> bool

pub fn iter(&self) -> impl Iterator<Item = &ChrEntry>

pub fn names(&self) -> Vec<String>

pub fn by_index(&self, index: usize) -> Option<&ChrEntry>

The chromosome the file numbers index, not the one at that position.

The two coincide on every file whose indices are dense and 0-based, which is every file any writer here or at UCSC produces — so the positional lookup is tried first and the walk is the fallback for a file that numbers its chromosomes otherwise.

pub fn genome_size(&self) -> i64

Total size of every chromosome, which is what a whole-genome walk covers.

pub fn get(&self, id: &str) -> Option<&ChrEntry>

pub fn contains(&self, id: &str) -> bool

pub fn resolve(&self, id: &str) -> Result<&ChrEntry>

Resolve a requested name, or fail with everything known about why not.

pub fn select(&self, requested: &[String]) -> Result<Vec<ChrEntry>>

Which chromosomes a request walks: the ones named, resolved, in the order they were asked for — or every chromosome in the file’s order when none were named.

Trait Implementations

impl Clone for ChrMap

fn clone(&self) -> ChrMap

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ChrMap

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

Formats the value using the given formatter.

impl Default for ChrMap

fn default() -> ChrMap

Returns the “default value” for a type.