https://github.com/bio-cr/bam-filter

Use simple expressions to filter a BAM/CRAM file
https://github.com/bio-cr/bam-filter

bam bioinformatics crystal genomics htslib

Last synced: about 2 months ago
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Use simple expressions to filter a BAM/CRAM file

• Host: GitHub
• URL: https://github.com/bio-cr/bam-filter
• Owner: bio-cr
• License: mit
• Created: 2022-01-19T07:35:21.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-02-10T00:33:11.000Z (over 1 year ago)
• Last Synced: 2025-05-08T19:03:09.155Z (5 months ago)
• Topics: bam, bioinformatics, crystal, genomics, htslib
• Language: C
• Homepage:
• Size: 63.5 KB
• Stars: 5
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Funding: .github/FUNDING.yml
  • License: LICENSE

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README

          
# bam-filter

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[Crystal](https://github.com/crystal-lang/crystal) implementation of [bam-filter](https://github.com/brentp/hts-nim-tools) by Brent Pedersen.

Filter BAM / CRAM / SAM files with a simple expression language.

## Installation

```sh

git clone https://github.com/bio-cr/bam-filter

make

sudo make install

```

- Ubuntu 20.04 and 22.04: deb packages are available from the [Github release page](https://github.com/bio-cr/bam-filter/releases).

  - Please note that installing the bam-filter deb package may uninstall packages that depend on `libcurl4-openssl-dev`, since `libhts-dev` depends on `libcurl4-gnutls-dev`.

- Currently only Linux is supported. Pull requests are welcome.

## Usage

```

Usage: bam-filter [options] 

    -e, --expression EXPR            eval code

    -o, --output PATH                Write output to FILE [standard output]

    -f, --fasta FASTA                Reference sequence FASTA FILE [null]

    -S, --sam                        Output SAM

    -b, --bam                        Output BAM

    -C, --cram                       Output CRAM (requires -f)

    -t, --threads NUM                Number of threads to use [0]

    --no-PG                          Do not add @PG line to the header

    -h, --help                       Show this help

    -v, --version                    Show version number

```

Example

```

bam-filter -S -e "chr=='chr1' && pos > 200 && tag_AS > 35" test/moo.bam

```

The given expression is evaluated by [klib/kexpr](https://attractivechaos.github.io/klib/#Kexpr%3A%20parsing%20mathematical%20expressions).

### Available values in expression

Fields: `name` `flag` `chr` `pos` `start` `stop` `mapq` `mchr` `mpos` `isize`

Flags: `paired` `proper_pair` `unmapped` `mate_unmapped`

`reverse` `mate_reverse` `read1` `read2` `secondary`

`qcfail` `duplicate` `supplementary`

Tags: `tag_XX` (XX is aux tag)

## Development

The easiest way to start development is to use [Gitpod](https://www.gitpod.io/). All you need is a browser.

## Contributing

Bug fixes and macOS support are welcome.

## Note

bam-filter was originally created to develop and test [HTS.cr](https://github.com/bio-cr/hts.cr).