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Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
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README.md

bamrescue AUR deb License Build status

bamrescue is a command line utility to check Binary Sequence Alignment / Map (BAM) files for corruption and rescue as much data as possible from them in the event they happen to be corrupted.

asciicast

Installation

On ArchLinux and derivatives (Manjaro, Antergos…)

A PKGBUILD is provided on AUR for ArchLinux and derivatives. It is only tested with an up-to-date ArchLinux.

# Get the PKGBUILD
git clone https://aur.archlinux.org/bamrescue.git

# Add the author's PGP key
gpg2 --recv-keys FA490B15D054C7E83F70B0408C145ABAC11FA702

# Build and install bamrescue
cd bamrescue
makepkg -si

Alternatively, you can install bamrescue using an AUR helper such as yay:

# Install bamrescue
yay -S bamrescue

On Debian and derivatives (Ubuntu, Mint…)

Pre-built packages are provided for Debian and derivatives. They are only tested with Debian 8 (Jessie), Debian 9 (Stretch), Ubuntu 16.04 LTS (Xenial) and Ubuntu 18.04 LTS (Bionic).

# Install prerequisites
sudo apt install curl apt-transport-https

# Add the author's PGP key
curl -s https://arkanosis.net/jroquet.pub.asc | sudo apt-key add -

# Add the author's apt stable channel to your apt sources
echo "deb https://apt.arkanosis.net/ software stable" | sudo tee /etc/apt/sources.list.d/arkanosis.list

# Update and install bamrescue
sudo apt update
sudo apt install bamrescue

Usage

Usage: bamrescue check [--quiet] [--threads=<threads>] <bamfile>
       bamrescue rescue [--threads=<threads>] <bamfile> <output>
       bamrescue -h | --help
       bamrescue --version

Commands:
    check                Check BAM file for corruption.
    rescue               Keep only non-corrupted blocks of BAM file.

Arguments:
    bamfile              BAM file to check or rescue.
    output               Rescued BAM file.

Options:
    -h, --help           Show this screen.
    -q, --quiet          Do not output statistics, stop at first error.
    --threads=<threads>  Number of threads to use, 0 for auto [default: 0].
    --version            Show version.

How it works

A BAM file is a BGZF file (specification), and as such is composed of a series of concatenated RFC1592-compliant gzip blocks (specification).

Each gzip block contains at most 64 KiB of data, including a CRC32 checksum of the uncompressed data which is used to check its integrity.

Additionally, since gzip blocks start with a gzip identifier (ie. 0x1f8b), a fixed gzip method (ie. 0x8) and fixed gzip flags (ie. 0x4), and bgzf blocks include both a bgzf identifier (ie. 0x4243), a fixed extra subfield length (ie. 0x2) and their own compressed size, it is possible to skip over corrupted blocks (at most 64 KiB) to the next non-corrupted block with limited complexity and acceptable reliability.

This property is used to rescue data from corrupted BAM files by keeping only their non-corrupted blocks, hopefully rescuing most reads.

Examples

A bam file of 40 MiB (which is very small by today standards) has been corrupted by two hard drive bad sectors. Most tools (including gzip) choke on the file at the first corrupted byte, meaning that up to 100% of the bam payload is considered lost depending on the tool.

Let's check the file using bamrescue:

$ bamrescue check samples/corrupted_payload.bam
bam file statistics:
   1870 bgzf blocks checked (117 MiB of bam payload)
      2 corrupted blocks found (0% of total)
     46 KiB of bam payload lost (0% of total)

Indeed, a whole hard drive bad sector typically amounts for 512 bytes lost, which is much smaller than an average bgzf block (which can be up to 64 KiB large).

Even though most tools would gave up on this file, it still contains almost 100% of non-corrupted bam payload, and the user probably wouldn't mind much if they could work only on that close-to-100% amount of data.

Let's rescue the non-corrupted payload (beware: this takes as much additional space on the disk as the original file):

$ bamrescue rescue samples/corrupted_payload.bam rescued_file.bam
bam file statistics:
   1870 bgzf blocks found (117 MiB of bam payload)
      2 corrupted blocks removed (0% of total)
     46 KiB of bam payload lost (0% of total)
   1868 non-corrupted blocks rescued (100% of total)
    111 MiB of bam payload rescued (100% of total)

The resulting bam file can now be used like if it never had been corrupted. Rescued data is validated using a CRC32 checksum, so it's not like ignoring errors and working on corrupted data (typical use of gzip to get garbage data from a corrupted bam file): it's working on (ridiculously) less, validated data.

Performance

bamrescue is very fast. Actually, it is even faster than gzip while doing more.

Here are some numbers for a 40 MiB, non-corrupted bam file:

Command Time Corruption detected
gzip -t 695 ms No
bamrescue check -q --threads=1 1181 ms No
bamrescue check -q --threads=2 661 ms No
bamrescue check -q --threads=4 338 ms No
bamrescue check --threads=1 1181 ms No
bamrescue check --threads=2 661 ms No
bamrescue check --threads=4 338 ms No

Chart

Here are some numbers for the same 40 MiB bam file, with two single-byte corruptions (at ~7 MiB and ~18 MiB, respectively):

Command Time Corruption detected Number of corrupted blocks reported Amount of data rescuable¹
gzip -t 93 ms Yes N/A 21 Mio (18%)
bamrescue check -q --threads=1 157 ms Yes N/A 21 Mio (18%)
bamrescue check -q --threads=2  91 ms Yes N/A 21 Mio (18%)
bamrescue check -q --threads=4  56 ms Yes N/A 21 Mio (18%)
bamrescue check --threads=1  1174 ms Yes 2 117 Mio (99.99%)
bamrescue check --threads=2  659 ms Yes 2 117 Mio (99.99%)
bamrescue check --threads=4  338 ms Yes 2 117 Mio (99.99%)

¹ uncompressed bam payload, rescued using gzip -d or bamrescue rescue

Chart

Note: these benchmarks have been run on an Intel Core i5-6500 CPU running Kubuntu 16.04.2 and rustc 1.18.0.

Caveats

bamrescue does not check whether the bam payload of the file is actually compliant with the bam specification. It only checks if it has not been corrupted after creation, using the error detection codes built in the gzip and bgzf formats. This means that as long as the tool used to create a bam file was compliant with the specification, the output of bamrescue will be as well, but bamrescue itself will do nothing to validate that compliance.

Compiling

Run cargo build --release in your working copy.

Contributing and reporting bugs

Contributions are welcome through GitHub pull requests.

Please report bugs and feature requests on GitHub issues.

License

bamrescue is copyright (C) 2017-2018 Jérémie Roquet jroquet@arkanosis.net and licensed under the ISC license.

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