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Cargo.toml

@@ -0,0 +1,10 @@
+[package]
+name = "insert_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"

src/main.rs

@@ -0,0 +1,40 @@
+use rust_htslib::{bam, bam::Read};
+use clap::Parser;
+
+#[derive(Parser, Debug)]
+#[command(author, version, about, long_about = None)]
+struct Args {
+    /// Name of the person to greet
+    #[arg(short, long)]
+    bam: String,
+
+    /// Number of times to greet
+    #[arg(short, long)]
+    position: String,
+}
+
+fn main() {
+    let args = Args::parse();
+    let bam = bam::Reader::from_path(&args.bam).unwrap();
+    let header = bam::Header::from_template(bam.header());
+
+    bam.fetch(("CHROMOSOME_I", 0, 20)).unwrap();
+
+    // pileup over all covered sites
+    for p in bam.pileup() {
+        let pileup = p.unwrap();
+        println!("{}:{} depth {}", pileup.tid(), pileup.pos(), pileup.depth());
+
+        for alignment in pileup.alignments() {
+            if !alignment.is_del() && !alignment.is_refskip() {
+                println!("Base {}", alignment.record().seq()[alignment.qpos().unwrap()]);
+            }
+            // mark indel start
+            match alignment.indel() {
+                bam::pileup::Indel::Ins(len) => println!("Insertion of length {} between this and next position.", len),
+                bam::pileup::Indel::Del(len) => println!("Deletion of length {} between this and next position.", len),
+                bam::pileup::Indel::None => ()
+            }
+        }
+    }
+}