wffilter

Filter over local alignments with a global alignment.

Compile

Fetch the source

[email protected]:urbanslug/wffilter.git
cd wffilter

cargo

Because this tool is written in Rust, the easiest way to compile it is using cargo. Find the cargo installation instructions here.

To install into the target/ dir.

cargo build --release
./target/release/wffilter -h

To install into the cargo binary path and your $PATH (assuming a standard rust setup).

cargo install --path .
wffilter -h

Usage

USAGE:
    wffilter [FLAGS] [OPTIONS] <input_paf>

FLAGS:
    -a, --adapt      To apply adaptive wavefront alignment [default: false]
    -h, --help       Prints help information
    -v               Sets the level of verbosity [default: 0]
    -V, --version    Prints version information

OPTIONS:
    -s, --segment-length <segment_length>    Segment length for aligning [default: 10]
    -t, --thread-count <thread_count>        Number of threads to use [default: 8]

ARGS:
    <input_paf>    Path to input PAF file

Example

wffilter -vv -a -s 100 x.paf > x.filtered.paf 

How it works

Match index

Reads a PAF file of local alignments from minimap2 or lastz and creates a cache from the match regions using coitrees.

Global alignment

This match index is then used by WFA to guide a global alignment through wflambda-rs in regions the size of the argument --segment-size/-s. This guidance involves querying the index to find out where matches are to fulfill the requirements of the match and traceback lambdas.

Known issues

I've currently disabled the effect of passing scoring penalties because it affects performance.

Citation

Santiago Marco-Sola, Juan Carlos Moure, Miquel Moreto, Antonio Espinosa. "Fast gap-affine pairwise alignment using the wavefront algorithm." Bioinformatics, 2020.