v1

positions.tsv

@@ -0,0 +1,2 @@
+chr1	47239294	47239298
+chr1	47239294	47239298

src/main.rs

@@ -1,35 +1,49 @@
+use std::{fs::File, io::{BufReader, BufRead}};
+
 use rust_htslib::{bam, bam::{Read, IndexedReader}};
 use clap::Parser;
 
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 struct Args {
-    /// Name of the perso≥n to greet
+    /// bam file path
     #[arg(short, long)]
     bam: String,
 
-    /// Number of times to greet
+    /// positions tsv path (seqname, start, end)
     #[arg(short, long)]
-    position: String,
+    positions: String,
 }
 
 fn main() {
     let args = Args::parse();
     let mut bam = bam::IndexedReader::from_path(&args.bam).unwrap();
 
-    // /Turbine-pool/LAL-T_ChIP/BAM/525/merged.bam
-    // /Turbine-pool/LAL-T_ChIP/BAM/885/merged.bam
-    let start = 47239294;
-    let end = 47239298;
+    let reader = BufReader::new(File::open(args.positions).unwrap());
+
+    let mut results: Vec<Result> = Vec::new();
+    for line in reader.lines() {
+        if let Ok(line) = line {
+            let mut split = line.split("\t");
+            results.extend(
+                fetch_ins(
+                    &mut bam, 
+                    split.next().unwrap(), 
+                    split.next().unwrap().parse().unwrap(),
+                    split.next().unwrap().parse().unwrap()
+                )
+            );
+        }
+    }
 
-    let results = fetch_ins(&mut bam, "chr1", start, end);
+    results.dedup();
 
     for result in results {
         println!("{}", result.tsv());
     }
 }
 
-#[derive(Debug)]
+#[derive(Debug, PartialEq)]
 struct Result {
     read_name: String,
     seqname: String,
@@ -98,13 +112,6 @@ fn fetch_ins(bam: &mut IndexedReader, seqname: &str, start: u32, end: u32) -> Ve
                         inserted_seq,
                         depth: pileup.depth()
                     });
-
-                    // println!(
-                    //     "{}\t{}:{}_{}ins[{}]\t{}",
-                    //     String::from_utf8_lossy(alignment.record().qname()),
-                    //     alignment.record().tid(), ref_pos, ref_pos + 1, inserted_seq,
-                    //     pileup.depth()
-                    // );
                 },
                 _ => ()
             }