filter-clipped

[Rust learning project]

Remove alignments with high number of clipped base.

Sometimes aligners have very loose scoring methods and write alignments with high abundant of soft/hard-clipped base into alignment BAM files. This program is for filtering these reads out by gating the number of clipped bases in relative to the read sequence length

Installation

``` $ git clone https://github.com/wckdouglas/filter-clipped $ cd filter-clipped $ cargo install --path . # if compilation error, try CC=/usr/bin/gcc cargo install --path . $ filter-clipped --help filter-clipped 0.1.0 Remove alignments with high number of clipped base. Sometimes aligner has very loose scoring methods and write alignments with high abundant of soft/hard-clipped base into alignment BAM files. This program is for filtering these reads out by gating the number of clipped bases in relative to the read sequence length

USAGE: filter-clipped [OPTIONS] --in-bam

OPTIONS: -b, --both-end maximum fraction of total bases on the sequence being clipped [default: 0.1] -h, --help Print help information -i, --in-bam input bam file path ("-" for stdin) --inverse keeping the failed ones (high-clipped-fraction alignments) -l, --left-side maximum fraction of bases on the sequence being clipped from the left side (5' end) [default: 0.1] -o, --out-bam output bam file path ("-" for stdout) [default: -] -r, --right-side maximum fraction of bases on the sequence being clipped from the right side (3' end) [default: 0.1] -V, --version Print version information ```

Test

cargo test

Docker

docker pull ghcr.io/wckdouglas/filter-clipped:main docker run --env RUST_LOG=info -v $PWD/:/root/ ghcr.io/wckdouglas/filter-clipped:main --in-bam /root/bamfile_in_current_path.bam | samtools view