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use super::bed;
use super::paf::*;
use colored::Colorize;
use itertools::Itertools;
use rayon::iter::ParallelBridge;
use rayon::prelude::*;
use rust_htslib::bam::record::Cigar::*;
use std::cmp;
pub enum Error {
PafParseCigar { msg: String },
PafParseCS { msg: String },
ParseIntError { msg: String },
ParsePafColumn {},
}
//type LiftoverResult<T> = Result<T, crate::liftover::Error>;
pub fn trim_paf_rec_to_rgn(rgn: &bed::Region, paf: &PafRecord) -> Option<PafRecord> {
// initialize a trimmed paf record
let mut trimmed_paf = paf.small_copy();
trimmed_paf.id = rgn.id.clone();
// check if we can return right away
if paf.t_st > rgn.st && paf.t_en < rgn.en {
return Some(paf.clone());
}
// index at the start of trimmed alignment
trimmed_paf.t_st = cmp::max(rgn.st, paf.t_st);
let start_idx = match paf.tpos_to_idx_match(trimmed_paf.t_st, true) {
Ok(idx) => idx,
Err(_) => panic!(
"\nProblem getting index in cigar:\n{}\n{}\n{}\n",
trimmed_paf.t_st, rgn, paf
),
};
// index at the end of trimmed alignment
trimmed_paf.t_en = cmp::min(rgn.en, paf.t_en);
// the end index is not inclusive so minus 1
let end_idx = match paf.tpos_to_idx_match(trimmed_paf.t_en - 1, false) {
Ok(idx) => idx,
Err(error_idx) => panic!(
"\nProblem getting index in cigar:\n{}\n{:?}\n{}\n{}\n",
trimmed_paf.t_en - 1,
&paf.tpos_aln[error_idx - 1],
rgn,
paf
),
};
// if this is the case then the whole internal regions is an indel
if start_idx > end_idx {
return None;
}
// update the start and end positions
trimmed_paf.t_st = paf.tpos_aln[start_idx];
trimmed_paf.q_st = paf.qpos_aln[start_idx];
trimmed_paf.t_en = paf.tpos_aln[end_idx];
trimmed_paf.q_en = paf.qpos_aln[end_idx];
// get the cigar opts
trimmed_paf.cigar = PafRecord::collapse_long_cigar(&paf.subset_cigar(start_idx, end_idx));
// make sure there are opts in the cigar that are not indels
let mut no_match_opts = true;
for opt in &trimmed_paf.cigar {
if matches!(opt, Match(_) | Equal(_) | Diff(_)) {
no_match_opts = false;
break;
}
}
if no_match_opts {
return None;
}
if paf.strand == '-' {
std::mem::swap(&mut trimmed_paf.q_en, &mut trimmed_paf.q_st);
}
// make end index not inclusive
trimmed_paf.t_en += 1;
trimmed_paf.q_en += 1;
// trim indels from start and end
trimmed_paf.remove_trailing_indels();
if trimmed_paf.cigar.len() == 0 {
return None;
}
if trimmed_paf.q_st > trimmed_paf.q_en || trimmed_paf.t_st > trimmed_paf.t_en {
eprintln!(
"Warning: liftover of {} failed. {} > {} or {} > {}",
rgn, trimmed_paf.q_st, trimmed_paf.q_en, trimmed_paf.t_st, trimmed_paf.t_en
);
return None;
}
// check that this is still a valid paf record
if let Err(e) = trimmed_paf.check_integrity() {
eprintln!("WARNING: {:?}", e);
return None;
};
Some(trimmed_paf)
}
pub fn trim_helper(name: &str, recs: &[PafRecord], rgns: &[bed::Region]) -> Vec<PafRecord> {
let mut cur_recs: Vec<PafRecord> = recs
.into_par_iter()
.filter(|rec| rec.t_name == name)
.map(|paf| (*paf).clone()) // clone the records so we can change them
.collect();
let cur_rgns: Vec<&bed::Region> = rgns
.into_par_iter()
.filter(|rgn| rgn.name == name)
.collect();
// calculated base by base liftover chain for each paf record
cur_recs
.par_iter_mut()
.for_each(|paf| (paf).aligned_pairs());
let cur_trimmed_paf: Vec<PafRecord> = cur_recs
.iter()
.cartesian_product(cur_rgns) // make all pairwise combs
.par_bridge()
.filter(|(paf, rgn)| paf.paf_overlaps_rgn(rgn)) //filter to overlapping pairs
.filter_map(|(paf, rgn)| trim_paf_rec_to_rgn(rgn, paf))
.collect();
cur_trimmed_paf
}
pub fn trim_paf_by_rgns(
rgns: &[bed::Region],
paf_recs: &[PafRecord],
invert_query: bool,
) -> Vec<PafRecord> {
// swap query and ref if needed.
let mut newvec = Vec::new();
let recs: &[PafRecord] = if invert_query {
for rec in paf_recs.iter() {
newvec.push(paf_swap_query_and_target(rec));
}
&newvec
} else {
paf_recs
};
// define the unique contig names to looks at
let names: Vec<&String> = recs.iter().map(|rec| &rec.t_name).unique().collect();
let mut trimmed_paf = Vec::new();
// iterate over one contigs name at a time
for (idx, name) in names.iter().enumerate() {
eprint!(
"\rProcessing contig {} {}/{} ",
name.bright_green().bold(),
idx + 1,
names.len()
);
let mut tmp = trim_helper(name, recs, rgns);
trimmed_paf.append(&mut tmp);
}
eprintln!();
trimmed_paf
}
/// # Example
/// ```
/// use rustybam::paf;
/// use rustybam::liftover;
/// let mut rec = paf::PafRecord::new("Q 10 0 10 + T 15 0 15 9 15 60 cg:Z:5=5D5=").unwrap();
/// let mut rec = paf::PafRecord::new("Q 15 0 15 + T 10 0 10 9 15 60 cg:Z:5=5I5=").unwrap();
/// let mut rec = paf::PafRecord::new("Q 15 0 15 - T 10 0 10 9 15 60 cg:Z:5=5I5=").unwrap();
/// rec.aligned_pairs();
/// for paf in liftover::break_paf_on_indels(&rec, 0){
/// eprintln!("{}", paf);
/// assert!(paf.t_en - paf.t_st == 5, "Incorrect size.");
/// }
/// ```
pub fn break_paf_on_indels(paf: &PafRecord, break_length: u32) -> Vec<PafRecord> {
let mut rtn = Vec::new();
let mut cur_tpos = paf.t_st;
let mut pre_tpos = paf.t_st;
for opt in paf.cigar.into_iter() {
let opt_len = opt.len();
if opt_len > break_length && matches!(opt, Del(_i) | Ins(_i)) {
if cur_tpos > pre_tpos {
let rgn = bed::Region {
name: paf.t_name.clone(),
st: pre_tpos,
en: cur_tpos,
id: paf.id.clone(),
..Default::default()
};
//rtn.push(trim_paf_rec_to_rgn(&rgn, paf));
if let Some(mut x) = trim_paf_rec_to_rgn(&rgn, paf) {
x.check_integrity().unwrap();
rtn.push(x)
}
}
pre_tpos = cur_tpos;
if consumes_reference(opt) {
pre_tpos += opt_len as u64;
}
}
if consumes_reference(opt) {
cur_tpos += opt_len as u64;
}
//eprintln!("{} {} {:?}", pre_tpos, cur_tpos, opt);
}
if cur_tpos > pre_tpos {
let rgn = bed::Region {
name: paf.t_name.clone(),
st: pre_tpos,
en: cur_tpos,
id: paf.id.clone(),
..Default::default()
};
if let Some(x) = trim_paf_rec_to_rgn(&rgn, paf) {
rtn.push(x)
}
}
rtn
}
#[cfg(test)]
mod tests {
use super::*;
use crate::bed::Region;
#[test]
fn test_aln_pair_liftover() {
println!(
"
/// Example alignment
/// 14-18 XXXXX
/// 0123456789012345567890....
/// ACTGACTGAAACTGAC-TAGA
/// ------------||||I|D||
/// TGACGT-AC
/// 01234567789 (forward)
/// XXXXX
/// 98765433210 (reverse)
"
);
let mut f_paf = PafRecord::new("Q 10 2 10 + T 40 12 20 3 9 60 cg:Z:4M1I1=1D2=").unwrap();
f_paf.aligned_pairs();
let mut r_paf = PafRecord::new("Q 10 2 10 - T 40 12 20 3 9 60 cg:Z:4M1I1=1D2=").unwrap();
r_paf.aligned_pairs();
let rgn = Region {
name: "T".to_string(),
st: 14,
en: 15,
id: "None".to_string(),
..Default::default()
};
let rgn2 = Region {
name: "T".to_string(),
st: 14,
en: 18,
id: "".to_string(),
..Default::default()
};
let rgn3 = Region {
name: "T".to_string(),
st: 12,
en: 20,
id: "".to_string(),
..Default::default()
};
// test right extend
let rgn4 = Region {
name: "T".to_string(),
st: 12,
en: 30,
id: "".to_string(),
..Default::default()
};
// test left extend
let rgn5 = Region {
name: "T".to_string(),
st: 5,
en: 20,
id: "".to_string(),
..Default::default()
};
// test both extend
let rgn6 = Region {
name: "T".to_string(),
st: 5,
en: 30,
id: "".to_string(),
..Default::default()
};
let sts = vec![4, 7, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2];
let ens = vec![5, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10];
let mut idx = 0;
for r in [rgn, rgn2, rgn3, rgn4, rgn5, rgn6] {
let trim = trim_paf_rec_to_rgn(&r, &f_paf).unwrap();
eprintln!("{}", trim);
eprintln!("{:?}", f_paf.tpos_aln);
eprintln!("{:?}", f_paf.qpos_aln);
eprintln!("{:?}", f_paf.long_cigar.to_string());
assert_eq!(trim.q_st, sts[idx]);
assert_eq!(trim.q_en, ens[idx]);
idx += 1;
eprintln!();
let trim = trim_paf_rec_to_rgn(&r, &r_paf).unwrap();
eprintln!("{}", trim);
eprintln!("{}", trim_paf_rec_to_rgn(&r, &r_paf).unwrap());
eprintln!("{:?}", r_paf.tpos_aln);
eprintln!("{:?}", r_paf.qpos_aln);
eprintln!("{:?}", f_paf.long_cigar.to_string());
assert_eq!(trim.q_st, sts[idx]);
assert_eq!(trim.q_en, ens[idx]);
idx += 1;
eprintln!("\n");
}
}
#[test]
/// this function tests that if we subset the ref and then invert that paf
/// we can get back the original ref subset.
fn check_invertible() {
/*
let mut paf = make_fake_paf_rec();
paf.aligned_pairs();
let rgn = Region {
name: "T".to_string(),
st: 14,
en: 17,
id: "None".to_string(),
};
let trim_paf = trim_paf_rec_to_rgn(&rgn, &paf);
eprintln!("{}", trim_paf);
let q_rgn = Region {
name: trim_paf.q_name.clone(),
st: trim_paf.q_st,
en: trim_paf.q_en,
id: "None".to_string(),
};
let mut trim_paf_swap = paf_swap_query_and_target(&trim_paf);
trim_paf_swap.aligned_pairs();
let ref_paf = paf_swap_query_and_target(&trim_paf_rec_to_rgn(&q_rgn, &trim_paf_swap));
// make sure we recreated what we wanted
assert_eq!(ref_paf.t_st, trim_paf.t_st);
assert_eq!(ref_paf.t_en, trim_paf.t_en);
assert_eq!(ref_paf.q_st, trim_paf.q_st);
assert_eq!(ref_paf.q_en, trim_paf.q_en);
assert_eq!(ref_paf.cigar, trim_paf.cigar);
eprintln!("{}", ref_paf);
*/
}
}