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use crate::{ gfa::{Line, Link, Path, Segment}, parser::GFAParser, }; use anyhow::{bail, Result}; use memmap::Mmap; use std::fs::File; use std::io::prelude::*; use bstr::ByteSlice; #[derive(Debug)] pub struct MmapGFA { pub cursor: std::io::Cursor<Mmap>, pub line_buf: Vec<u8>, pub current_line_len: usize, pub last_buf_offset: usize, pub parser: GFAParser<usize, ()>, } #[derive(Debug, Clone, Copy, PartialEq, Eq)] pub enum LineType { Segment, Link, Path, } #[derive(Debug, Clone, PartialEq, Eq)] pub struct LineIndices { pub segments: Vec<(usize, usize)>, pub links: Vec<usize>, pub paths: Vec<usize>, } #[derive(Debug)] pub struct SegmentIter<'a> { mmap: &'a mut MmapGFA, parser: GFAParser<usize, ()>, } impl<'a> Iterator for SegmentIter<'a> { type Item = Segment<usize, ()>; #[inline] fn next(&mut self) -> Option<Self::Item> { while let Ok(line) = self.mmap.next_line() { if let Some(b'S') = line.first() { if let Some(Line::Segment(s)) = self.parser.parse_gfa_line(line).ok() { return Some(s); } } } None } } #[derive(Debug)] pub struct LinkIter<'a> { mmap: &'a mut MmapGFA, parser: GFAParser<usize, ()>, } impl<'a> Iterator for LinkIter<'a> { type Item = Link<usize, ()>; #[inline] fn next(&mut self) -> Option<Self::Item> { while let Ok(line) = self.mmap.next_line() { if let Some(b'S') = line.first() { if let Some(Line::Link(s)) = self.parser.parse_gfa_line(line).ok() { return Some(s); } } } None } } #[derive(Debug)] pub struct PathIter<'a> { mmap: &'a mut MmapGFA, parser: GFAParser<usize, ()>, } impl<'a> Iterator for PathIter<'a> { type Item = Path<usize, ()>; #[inline] fn next(&mut self) -> Option<Self::Item> { while let Ok(line) = self.mmap.next_line() { if let Some(b'S') = line.first() { if let Some(Line::Path(s)) = self.parser.parse_gfa_line(line).ok() { return Some(s); } } } None } } impl MmapGFA { pub fn new(path: &str) -> Result<Self> { let file = File::open(path)?; let mmap = unsafe { Mmap::map(&file)? }; let cursor = std::io::Cursor::new(mmap); let line_buf = Vec::with_capacity(1024); let current_line_len = 0; let last_buf_offset = 0; let parser = GFAParser::new(); Ok(Self { cursor, line_buf, current_line_len, last_buf_offset, parser, }) } pub fn reset_position(&mut self) -> u64 { let cur_pos = self.cursor.position(); self.cursor.set_position(0); cur_pos } pub fn set_position(&mut self, new_pos: u64) -> u64 { let cur_pos = self.cursor.position(); self.cursor.set_position(new_pos); cur_pos } pub fn get_ref(&self) -> &[u8] { self.cursor.get_ref().as_ref() } pub fn get_parser(&self) -> &GFAParser<usize, ()> { &self.parser } pub fn next_line(&mut self) -> Result<&[u8]> { self.line_buf.clear(); self.last_buf_offset = self.cursor.position() as usize; let n_read = self.cursor.read_until(b'\n', &mut self.line_buf)?; self.current_line_len = n_read; Ok(&self.line_buf[..n_read]) } pub fn read_line_at(&mut self, offset: usize) -> Result<&[u8]> { self.cursor.set_position(offset as u64); self.next_line() } pub fn build_index(&mut self) -> Result<LineIndices> { let start_position = self.cursor.position(); let current_line_len = self.current_line_len; let last_buf_offset = self.last_buf_offset; let mut segments = Vec::new(); let mut links = Vec::new(); let mut paths = Vec::new(); self.cursor.set_position(0); let mut line_start = 0; loop { let line = self.next_line()?; let length = line.len(); if let Some(ref byte) = line.first() { match byte { b'S' => { segments.push((line_start, length)); } b'L' => { links.push(line_start); } b'P' => { paths.push(line_start); } _ => (), }; line_start += line.len(); } else { break; } } self.cursor.set_position(start_position); self.current_line_len = current_line_len; self.last_buf_offset = last_buf_offset; let res = LineIndices { segments, links, paths, }; Ok(res) } pub fn current_line(&self) -> &[u8] { &self.line_buf[..self.current_line_len] } pub fn current_line_name(&self) -> Option<&[u8]> { let mut iter = self.line_buf.split_str("\t"); let _lt = iter.next()?; let name = iter.next()?; Some(name) } pub fn parse_current_line(&self) -> Result<Line<usize, ()>> { let line = self.current_line(); if line.is_empty() { bail!("Line at offset {} is empty", self.last_buf_offset); } let gfa_line = self.parser.parse_gfa_line(line)?; Ok(gfa_line) } pub fn iter_segments(&mut self, from_start: bool) -> SegmentIter<'_> { if from_start { self.cursor.set_position(0); } let parser = self.parser.clone(); SegmentIter { mmap: self, parser } } pub fn iter_links(&mut self, from_start: bool) -> LinkIter<'_> { if from_start { self.cursor.set_position(0); } let parser = self.parser.clone(); LinkIter { mmap: self, parser } } pub fn iter_paths(&mut self, from_start: bool) -> PathIter<'_> { if from_start { self.cursor.set_position(0); } let parser = self.parser.clone(); PathIter { mmap: self, parser } } }