https://github.com/biojulia/pairwisemappingformat.jl

Parser for the PAF format in bioinformatics
https://github.com/biojulia/pairwisemappingformat.jl

Last synced: 11 months ago
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Parser for the PAF format in bioinformatics

• Host: GitHub
• URL: https://github.com/biojulia/pairwisemappingformat.jl
• Owner: BioJulia
• License: mit
• Created: 2024-06-14T18:47:17.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2025-02-25T15:18:44.000Z (over 1 year ago)
• Last Synced: 2025-04-15T21:22:43.588Z (about 1 year ago)
• Language: Julia
• Size: 290 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
#  PairwiseMappingFormat

[![Latest Release](https://img.shields.io/github/release/BioJulia/PairwiseMappingFormat.jl.svg)](https://github.com/BioJulia/PairwiseMappingFormat.jl/releases/latest)

[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/PairwiseMappingFormat.jl/blob/master/LICENSE)

[![Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/PairwiseMappingFormat.jl/dev)

[![](https://codecov.io/gh/BioJulia/PairwiseMappingFormat.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/PairwiseMappingFormat.jl)

PairwiseMappingFormat.jl provide a parser for Pairwise Mapping Format (PAF) files.

PAF is a simple, tab-delimited format created by programs such as minimap2.

To learn how to use the package, [read the documentation](https://biojulia.github.io/PairwiseMappingFormat.jl/dev/)

## Example

```julia

PAFReader(open("file.paf")) do reader

    for record in reader

        if aln_identity(record) > 0.95 && record.alnlen > 2_000

            println(record.qname, " aligns well to ", record.tname)

        end

    end

end

```

## Installation

Install PairwiseMappingFormat.jl from the julia

REPL. Press `]` to enter Pkg mode, and enter the following:

```julia

add PairwiseMappingFormat

```

## Contributing

Make an issue or PR on this repository, or get in touch with the BioJulia community over at the [Julia Slack](https://julialang.org/slack/) or Zulip servers.