Rust Htslib

https://docs.rs/rust_htslib/1.0.0/rust_htslib/
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Rust Htslib is a high-level Rust API for reading and writing common HTS (High-Throughput Sequencing)...
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### Fetch Specific Region from Indexed BAM in Rust

Source: https://docs.rs/rust_htslib

Demonstrates how to use `fetch` with an `IndexedReader` to constrain reads or pileups to a specific genomic region. Requires an indexed BAM file.

```rust
use rust_htslib::{bam, bam::Read};

let mut bam = bam::IndexedReader::from_path(&"test/test.bam").unwrap();

bam.fetch(("CHROMOSOME_I", 0, 20)).unwrap();
// afterwards, read or pileup in this region
```

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### Copy Reverse Reads to New BAM File in Rust

Source: https://docs.rs/rust_htslib

Reads a BAM file and writes only the reverse reads to a new BAM file. Requires a header template from the original file.

```rust
use rust_htslib::{bam, bam::Read};

let mut bam = bam::Reader::from_path(&"test/test.bam").unwrap();
let header = bam::Header::from_template(bam.header());
let mut out = bam::Writer::from_path(&"test/out.bam", &header, bam::Format::Bam).unwrap();

// copy reverse reads to new BAM file
for r in bam.records() {
    let record = r.unwrap();
    if record.is_reverse() {
        out.write(&record).unwrap();
    }
}
```

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### Read BAM Header in Rust

Source: https://docs.rs/rust_htslib

Reproduces the functionality of 'samtools view -H'. Reads a BAM file and prints its header records to the terminal.

```rust
use rust_htslib::{bam, bam::Read};


let bam = bam::Reader::from_path(&"test/test.bam").unwrap();
let header = bam::Header::from_template(bam.header());

// print header records to the terminal, akin to samtool
for (key, records) in header.to_hashmap() {
    for record in records {
         println!("@{{}}	SN:{{}}	LN:{{}}", key, record["SN"], record["LN"]);
    }
}
```

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### Perform Pileup on BAM File in Rust

Source: https://docs.rs/rust_htslib

Iterates through all covered sites in a BAM file, printing depth and base information for each alignment. Handles insertions and deletions.

```rust
use rust_htslib::{bam, bam::Read};

let mut bam = bam::Reader::from_path(&"test/test.bam").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 => ()
        }
    }
}
```
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