rust_htslib/bcf/

buffer.rs

// Copyright 2017 Johannes Köster.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.

use std::cmp::Ordering;
use std::collections::{vec_deque, VecDeque};
use std::mem;

use crate::bcf::{self, Read};
use crate::errors::Result;

/// A buffer for BCF records. This allows access regions in a sorted BCF file while iterating
/// over it in a single pass.
/// The buffer is implemented as a ringbuffer, such that extension or movement to the right has
/// linear complexity. The buffer does not use any indexed random access. Hence, for getting a
/// region at the very end of the BCF, you will have to wait until all records before have
/// been read.
#[derive(Debug)]
pub struct RecordBuffer {
    reader: bcf::Reader,
    ringbuffer: VecDeque<bcf::Record>,
    ringbuffer2: VecDeque<bcf::Record>,
    overflow: Option<bcf::Record>,
}

unsafe impl Sync for RecordBuffer {}
unsafe impl Send for RecordBuffer {}

impl RecordBuffer {
    /// Create new buffer.
    pub fn new(reader: bcf::Reader) -> Self {
        RecordBuffer {
            reader,
            ringbuffer: VecDeque::new(),
            ringbuffer2: VecDeque::new(),
            overflow: None,
        }
    }

    fn last_rid(&self) -> Option<u32> {
        self.ringbuffer.back().map(|rec| rec.rid().unwrap())
    }

    fn next_rid(&self) -> Option<u32> {
        self.ringbuffer2.back().map(|rec| rec.rid().unwrap())
    }

    fn swap_buffers(&mut self) {
        // swap with buffer for next rid
        mem::swap(&mut self.ringbuffer2, &mut self.ringbuffer);
        // clear second buffer
        self.ringbuffer2.clear();
    }

    fn drain_left(&mut self, rid: u32, window_start: u64) -> usize {
        // remove records too far left or from wrong rid
        // rec.rid() will always yield Some(), because otherwise we won't put the rec into the
        // buffer.
        let to_remove = self
            .ringbuffer
            .iter()
            .take_while(|rec| (rec.pos() as u64) < window_start || rec.rid().unwrap() != rid)
            .count();
        self.ringbuffer.drain(..to_remove);
        to_remove
    }

    /// Fill the buffer with variants in the given window. The start coordinate has to be right of
    /// the start coordinate of any previous `fill` operation.
    /// Coordinates are 0-based, and end is exclusive.
    /// Returns tuple with numbers of added and deleted records compared to previous fetch.
    pub fn fetch(&mut self, chrom: &[u8], start: u64, end: u64) -> Result<(usize, usize)> {
        // TODO panic if start is left of previous start or we have moved past the given chrom
        // before.
        let rid = self.reader.header.name2rid(chrom)?;
        let mut added = 0;
        let mut deleted = 0;

        // shrink and swap
        match (self.last_rid(), self.next_rid()) {
            (Some(last_rid), _) => {
                if last_rid != rid {
                    deleted = self.ringbuffer.len();
                    self.swap_buffers();
                    added = self.ringbuffer.len();
                // TODO drain left?
                } else {
                    deleted = self.drain_left(rid, start);
                }
            }
            (_, Some(_)) => {
                // TODO is this really necessary? If there was no fetch before, there is nothing
                // to delete.
                deleted = self.ringbuffer.len();
                self.swap_buffers();
                deleted += self.drain_left(rid, start);
                added = self.ringbuffer.len();
            }
            _ => (),
        }

        if !self.ringbuffer2.is_empty() {
            // We have already read beyond the current rid. Hence we can't extend to the right for
            // this rid.
            return Ok((added, deleted));
        }

        // move overflow from last fill into ringbuffer
        if self.overflow.is_some() {
            let pos = self.overflow.as_ref().unwrap().pos() as u64;
            if pos >= start {
                if pos <= end {
                    self.ringbuffer.push_back(self.overflow.take().unwrap());
                    added += 1;
                } else {
                    return Ok((added, deleted));
                }
            } else {
                // discard overflow
                self.overflow.take();
            }
        }

        // extend to the right
        loop {
            let mut rec = self.reader.empty_record();

            if self.reader.read(&mut rec).is_none() {
                // EOF
                break;
            }
            let pos = rec.pos() as u64;
            if let Some(rec_rid) = rec.rid() {
                match rec_rid.cmp(&rid) {
                    Ordering::Equal => {
                        if pos >= end {
                            // Record is beyond our window. Store it anyways but stop.
                            self.overflow = Some(rec);
                            break;
                        } else if pos >= start {
                            // Record is within our window.
                            self.ringbuffer.push_back(rec);
                            added += 1;
                        } else {
                            // Record is upstream of our window, ignore it
                            continue;
                        }
                    }
                    Ordering::Greater => {
                        // record comes from next rid. Store it in second buffer but stop filling.
                        self.ringbuffer2.push_back(rec);
                        break;
                    }
                    _ => {
                        // Record comes from previous rid. Ignore it.
                        continue;
                    }
                }
            } else {
                // skip records without proper rid
                continue;
            }
        }

        Ok((added, deleted))
    }

    /// Iterate over records that have been fetched with `fetch`.
    pub fn iter(&self) -> vec_deque::Iter<'_, bcf::Record> {
        self.ringbuffer.iter()
    }

    /// Iterate over mutable references to records that have been fetched with `fetch`.
    pub fn iter_mut(&mut self) -> vec_deque::IterMut<'_, bcf::Record> {
        self.ringbuffer.iter_mut()
    }

    pub fn len(&self) -> usize {
        self.ringbuffer.len()
    }

    pub fn is_empty(&self) -> bool {
        self.len() == 0
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::bcf;

    #[test]
    fn test_buffer() {
        let reader = bcf::Reader::from_path(&"test/test.bcf").unwrap();
        let mut buffer = RecordBuffer::new(reader);

        buffer.fetch(b"1", 100, 10023).unwrap();
        {
            let records: Vec<_> = buffer.iter().collect();
            assert_eq!(records.len(), 2);
            assert_eq!(records[0].pos(), 10021);
            assert_eq!(records[1].pos(), 10022);
        }

        buffer.fetch(b"1", 10023, 10024).unwrap();
        {
            let records: Vec<_> = buffer.iter().collect();
            assert_eq!(records.len(), 1);
            assert_eq!(records[0].pos(), 10023);
        }
    }
}