rsomics-bam-quickcheck

Quickly validate that one or more BAM files appear intact — a Rust port of samtools quickcheck. Checks: (1) BGZF magic at the start, (2) BAM\1 header magic after decompressing the first BGZF block, (3) the 28-byte BGZF EOF marker at the end. Exits non-zero if any file fails.

Install

cargo install rsomics-bam-quickcheck

Usage

rsomics-bam-quickcheck file.bam                # exit 0 = OK
rsomics-bam-quickcheck *.bam                   # check many; exit non-zero on any failure
rsomics-bam-quickcheck -v file.bam             # also print one-line diagnostic per failure
rsomics-bam-quickcheck -u file.bam             # skip the EOF check

Origin

Independent Rust reimplementation of samtools quickcheck. samtools is MIT-licensed; the precise BGZF EOF marker bytes, the BAM\1 header magic, and the silent-by-default exit-code convention were determined from samtools' MIT-licensed source plus the SAM/BAM and BGZF specifications.

License: MIT OR Apache-2.0. Upstream credit: samtools (MIT).