Struct IntervalSet 

pub struct IntervalSet { /* private fields */ }

A collection of genomic intervals with overlap query support.

Queries use O(n) linear scan by default. Call IntervalSet::build_index() to construct per-chromosome interval trees for O(log n + k) queries.

Implementations

impl IntervalSet

pub fn new() -> Self

Create an empty interval set.

pub fn from_intervals(intervals: Vec<GenomicInterval>) -> Self

Create an interval set from existing intervals.

pub fn push(&mut self, interval: GenomicInterval)

Add an interval. Marks the set as unsorted and invalidates the index.

pub fn len(&self) -> usize

Number of intervals in the set.

pub fn is_empty(&self) -> bool

Whether the set is empty.

pub fn sort(&mut self)

Sort intervals by chromosome then start position.

pub fn build_index(&mut self)

Build per-chromosome interval tree indices for O(log n + k) queries.

This is called automatically on first query if the set is sorted, but can also be called explicitly. Invalidated by push().

pub fn overlapping(&self, query: &GenomicInterval) -> Vec<&GenomicInterval>

Return all intervals that overlap the query.

Uses the interval tree index if available, otherwise falls back to O(n) scan.

pub fn containing(&self, chrom: &str, position: u64) -> Vec<&GenomicInterval>

Return all intervals containing a given position.

Uses the interval tree index if available, otherwise falls back to O(n) scan.

pub fn merge_overlapping(&self) -> IntervalSet

Merge all overlapping intervals and return a new, sorted set.

Adjacent intervals on the same chromosome that overlap or abut are merged into a single interval.

pub fn intervals(&self) -> &[GenomicInterval]

Borrow the intervals as a slice.

pub fn into_intervals(self) -> Vec<GenomicInterval>

Consume the set and return the inner intervals.

pub fn coverage(&self, chrom: &str) -> u64

Total bases covered on a given chromosome (after merging overlaps).

Trait Implementations

impl Default for IntervalSet

fn default() -> Self

Returns the “default value” for a type.

impl Summarizable for IntervalSet

fn summary(&self) -> String

A one-line summary suitable for display.