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pub mod builder;
pub mod header;
mod indexer;
pub mod reference_sequence;
pub use self::{
builder::Builder, header::Header, indexer::Indexer, reference_sequence::ReferenceSequence,
};
use std::{
io,
ops::{Bound, RangeBounds},
};
use indexmap::IndexSet;
use noodles_csi::{
binning_index::optimize_chunks, index::reference_sequence::bin::Chunk, BinningIndex,
};
pub type ReferenceSequenceNames = IndexSet<String>;
#[derive(Debug)]
pub struct Index {
header: Header,
reference_sequence_names: ReferenceSequenceNames,
reference_sequences: Vec<ReferenceSequence>,
unplaced_unmapped_record_count: Option<u64>,
}
impl Index {
pub fn builder() -> Builder {
Builder::default()
}
pub fn indexer() -> Indexer {
Indexer::default()
}
pub fn header(&self) -> &Header {
&self.header
}
pub fn reference_sequence_names(&self) -> &ReferenceSequenceNames {
&self.reference_sequence_names
}
#[deprecated(
since = "0.2.0",
note = "Use `unplaced_unmapped_record_count` instead."
)]
pub fn unmapped_read_count(&self) -> Option<u64> {
self.unplaced_unmapped_record_count
}
}
impl BinningIndex<ReferenceSequence> for Index {
fn reference_sequences(&self) -> &[ReferenceSequence] {
&self.reference_sequences
}
fn unplaced_unmapped_record_count(&self) -> Option<u64> {
self.unplaced_unmapped_record_count
}
fn query<B>(&self, reference_sequence_id: usize, interval: B) -> io::Result<Vec<Chunk>>
where
B: RangeBounds<i32> + Clone,
{
let reference_sequence = self
.reference_sequences()
.get(reference_sequence_id)
.ok_or_else(|| {
io::Error::new(
io::ErrorKind::InvalidInput,
format!("invalid reference sequence ID: {}", reference_sequence_id),
)
})?;
let query_bins = reference_sequence
.query(interval.clone())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
let chunks: Vec<_> = query_bins
.iter()
.flat_map(|bin| bin.chunks())
.copied()
.collect();
let start = match interval.start_bound() {
Bound::Included(s) => *s,
Bound::Excluded(s) => *s + 1,
Bound::Unbounded => 1,
};
let min_offset = reference_sequence.min_offset(start);
let merged_chunks = optimize_chunks(&chunks, min_offset);
Ok(merged_chunks)
}
}
impl Default for Index {
fn default() -> Self {
Builder::default().build()
}
}