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Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "indl_finder"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+clap = { version = "4.2.4", features = ["derive"] }
+rust-htslib = "0.42.0"
+merge_sequences  = { git = "https://github.com/Dr-TSteimle/merge_sequences" }
+desc_sequence    = { git = "https://git.t0m4.fr/Thomas/desc_sequence.git" }
+rand = "0.8.5"
+itertools = "0.10.5"

src/main.rs

@@ -0,0 +1,200 @@
+use std::{io::{BufReader, BufRead}, fs::File, collections::HashMap, cmp};
+
+use rust_htslib::{bam, bam::{Read, IndexedReader}};
+use clap::Parser;
+use rand::{thread_rng, seq::SliceRandom};
+use itertools::Itertools;
+
+use merge_sequences::*;
+use desc_sequence::*;
+#[derive(Parser, Debug)]
+#[command(author, version, about, long_about = None)]
+struct Args {
+    /// bam file path
+    #[arg(short, long)]
+    bam: String,
+
+    /// positions tsv path (seqname, start, end)
+    #[arg(short, long)]
+    positions: String,
+}
+
+fn main() {
+    let args = Args::parse();
+    let mut bam = bam::IndexedReader::from_path(&args.bam).unwrap();
+
+    let reader = BufReader::new(File::open(args.positions).unwrap());
+
+    for line in reader.lines() {
+        if let Ok(line) = line {
+            let mut split = line.split("\t");
+            select_reads(
+                &mut bam, 
+                (split.next().unwrap(), 
+                split.next().unwrap().parse().unwrap(),
+                split.next().unwrap().parse().unwrap())
+            );
+        }
+    }
+}
+
+fn select_reads(bam: &mut IndexedReader, range: (&str, i64, i64)) {
+    let merge_dist = 1;
+    let _ = bam.fetch(range);
+    
+    let mut seqs = Vec::new();
+
+    for read in bam.records() {
+        if let Ok(read) = read {
+            let cigar_str: desc_sequence::Cigar = Cigar::new_from_str(&read.cigar().to_string());
+            let qname = String::from_utf8(read.qname().to_vec()).unwrap();
+            
+            for cigar_item in read.cigar().iter() {
+                match cigar_item {
+                    bam::record::Cigar::Match(_) => (),
+                    bam::record::Cigar::Del(_) | bam::record::Cigar::Ins(_) => {
+                        let dnas = read.seq().as_bytes();
+                        if !dnas.contains(&b'N') { // conversion doesnt work with N TODO
+                            let (del, ins) = find_deletion_insertion_ranges(read.pos() as u32, cigar_str.clone(), read.is_reverse());
+                            
+                            del.into_iter().for_each(|(start, end)| {
+                                seqs.push((qname.to_string(), "del".to_string(), start, end, DNAString::new(read.seq().as_bytes())));
+                            });
+
+                            ins.into_iter().for_each(|(start, end)| {
+                                seqs.push((qname.to_string(), "ins".to_string(), start, end, DNAString::new(read.seq().as_bytes())));
+                            });
+                        }
+                    },
+                    bam::record::Cigar::RefSkip(_) => (),
+                    bam::record::Cigar::SoftClip(_) => (),
+                    bam::record::Cigar::HardClip(_) => (),
+                    bam::record::Cigar::Pad(_) => (),
+                    bam::record::Cigar::Equal(_) => (),
+                    bam::record::Cigar::Diff(_) => (),
+                }
+            }
+        }
+    }
+    seqs.sort_by(|a, b| {
+        a.2.cmp(&b.2)
+    });
+
+    let mut grouped: HashMap<i32, (u32, u32, Vec<String>, Vec<DNAString>)> = HashMap::new();
+
+    let mut last_key = None;
+
+    for seq in seqs {
+        if let Some(lk) = last_key {
+            let last = grouped.get_mut(&lk).unwrap();
+
+            if last.1 + merge_dist >= seq.2 {
+                last.1 = cmp::max(last.1, seq.2);
+                last.2.push(seq.0);
+                last.3.push(seq.4)
+            } else {
+                let nk = lk + 1;
+                last_key = Some(nk);
+                grouped.insert(nk, (seq.2, seq.3, vec![seq.0], vec![seq.4]));
+                
+            }
+        } else {
+            last_key = Some(0);
+            grouped.insert(0, (seq.2, seq.3, vec![seq.0], vec![seq.4]));
+        }
+    }
+
+    grouped.iter().for_each(|(k, e)| {
+        println!("{}", k);
+        println!("{:?}", e);
+    });
+
+    println!("=====================================");
+
+    let aligner = BwaAlign::init("/home/thomas/NGS/tools/arriba_v2.1.0/hg38viral.fa");
+    for (k, group) in grouped {
+        println!("{}", k);
+        let res = rec_merger(group.3, 15, 2, 1 as i8);
+
+        res.iter().for_each(|s| {
+            let r = aligner.get_ref_positions_indel(&s.as_string());
+            println!("{:?}", r);
+        });
+
+        
+    }
+
+    // 
+    // for s in res.iter() {
+    //     println!("{}", &s.as_string());
+    //     let r = aligner.get_ref_positions_indel(&s.as_string());
+
+    //     r.iter().for_each(|e| {
+    //         println!("{:?}", e);
+    //     })
+
+    // }
+
+}
+
+pub fn rec_merger(mut seqs: Vec<DNAString>, kmer_len: usize, max_mismatches: i8, max_consecutive_mismatches: i8) -> Vec<DNAString> {
+    let mut n_retry = 0;
+
+    let mut merged = Vec::new();
+    let mut last_len = seqs.len();
+    loop {
+        if last_len <= 1 { break; }
+
+        let tmp = seqs.get(1..).unwrap().to_vec();
+        let re = merger(&tmp, seqs.get(0).unwrap(), kmer_len, max_mismatches, max_consecutive_mismatches);
+        match re {
+            Some(res) => {
+                merged.push(res.0.clone());
+                // res.1.append(&mut vec![res.0]);
+                seqs = res.1;
+            },
+            None => {
+                match n_retry {
+                    0 => seqs.reverse(),
+                    _ => seqs.shuffle(&mut thread_rng())
+                }
+            },
+        }
+        n_retry += 1;
+
+        if last_len == seqs.len() {
+            break;
+        } else {
+            last_len = seqs.len();
+        }
+    }
+    merged
+}
+
+
+pub fn merger(sequences: &Vec<DNAString>, to_merge: &DNAString, kmer_len: usize, max_mismatches: i8, max_consecutive_mismatches: i8) -> Option<(DNAString, Vec<DNAString>)> {
+    let mut to_merge = to_merge.clone();
+    let mut merged = Vec::new();
+
+    // try to merge to others seeds
+    for (i, seed) in sequences.iter().enumerate() {
+        if seed.0.len() >= kmer_len {
+            let r = to_merge.merge(seed, kmer_len, max_mismatches, max_consecutive_mismatches);
+            match r {
+                Ok(_) => {
+                    merged.push(i);
+                },
+                Err(_err) => (),
+            }
+        }
+    }
+    
+    if merged.len() > 0 {
+        Some((
+            to_merge,
+            sequences.into_iter().enumerate().filter(|(i, _)| !merged.contains(i)).map(|(_, e)| e.clone()).collect::<Vec<DNAString>>()
+        ))
+    } else {
+        None
+    }
+}

test.tsv

@@ -0,0 +1 @@
+chr1	47225827	47225943