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Installation

From crates.io

cargo install bedpull

Build from source

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.

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).
  • 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).