bedpull 0.2.0

bedpull - Pull the query sequence from bam or fasta references using a bed file
Documentation 
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# Installation

## From crates.io

```bash
cargo install bedpull
```

## Build from source

```bash
git clone https://github.com/Psy-Fer/bedpull
cd bedpull
cargo build --release
./target/release/bedpull --help
```

## Static binary for HPC (musl)

Cluster environments often run older glibc versions that are incompatible with binaries built on a modern workstation. Building with the `x86_64-unknown-linux-musl` target produces a fully static binary with no shared library dependencies.

```bash
rustup target add x86_64-unknown-linux-musl
RUSTFLAGS='-C link-arg=-s' cargo build --release --target x86_64-unknown-linux-musl
```

The binary is at `target/x86_64-unknown-linux-musl/release/bedpull`. Copy it to your HPC login node or scratch space; it requires no runtime dependencies.

## Requirements

- Rust 1.85 or later (edition 2024; install via [rustup](https://rustup.rs)).
- A coordinate-sorted BAM for BAM mode, or a CRAM (optionally with `--reference` for
  reference-compressed CRAMs) for CRAM mode. If the `.bai`/`.crai` index is missing, bedpull
  builds it automatically the first time you run against that file, so `samtools` is not required.
- A FASTA for PAF mode query extraction (`--query_ref`) or CRAM reference decoding
  (`--reference`). If the `.fai` index is missing, bedpull builds it automatically too.
- A PAF file for PAF mode; the PAF must include the `cg:Z:` CIGAR tag (produced by `minimap2 -c` or `--cs=long`).