jdidion

I am a programmer and bioinformatician. I develop and contribute to several open-source genomics projects.

AptonLivermore, CA

Pinned Repositories

atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Language:Python121 8 11815
autoclick
Create Click-based CLIs from python3 type annotations (beta)
Language:Python12 3 103
beekeeper
A worker pool library for Rust
Language:Rust11 1 40
biotools
A list of useful bioinformatics resources
600 39 2169
feedme
A simple, flexible, and extensible RSS and Atom parser for Ruby. Based on the popular SimpleRSS library, but with many nice extra features. (retired)
Language:Ruby8 4 00
pairwise-alignment
Catalogue of pairwise alignment algorithms and benchmarks
Language:Rust25 1 00
pest-test
Testing framework for pest parser (similar to `tree-sitter test`)
Language:Rust10 2 43
wdl-rs
Rust parser for Workflow Description Language (WDL)
Language:Rust5 3 00
xphyle
Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)
Language:Python21 3 243
Zooper
Zotero plugin for updating metadata and managing PDFs. (alpha)
Language:JavaScript13 5 00

jdidion's Repositories

jdidion/biotools
A list of useful bioinformatics resources
600 39 2169
jdidion/atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Language:Python121 8 11815
jdidion/pairwise-alignment
Catalogue of pairwise alignment algorithms and benchmarks
Language:Rust25 1 00
jdidion/xphyle
Python library that facilitates opening, reading, and writing files (and file-like entities like URLs and streams) agnostic of compression format. (production)
Language:Python21 3 243
jdidion/beekeeper
A worker pool library for Rust
Language:Rust11 1 40
jdidion/pest-test
Testing framework for pest parser (similar to `tree-sitter test`)
Language:Rust10 2 43
jdidion/wdl-rs
Rust parser for Workflow Description Language (WDL)
Language:Rust5 3 00
jdidion/subby
Python subprocesses simplified.
Language:Python2 3 1
jdidion/tree-sitter-wdl
Tree-sitter grammar for WDL (Workflow Description Language)
Language:C2 2 11
jdidion/cwl-v1.2
Released CWL v1.2 specification
Language:Common Workflow Language1 2 0
jdidion/jdidion.github.io
Language:SCSS1 3 0
jdidion/pest-wdl
Pest parser grammar for Workflow Description Language (WDL)
Language:wdl1 2 0
jdidion/pytest-datadir-nng
The *next* next generation of python-datadir
Language:Python1 2 0
jdidion/cachier
Persistent, stale-free, local and cross-machine caching for Python functions.
Language:Python1 0
jdidion/FuBAR
Fun with Bioinformatics Algorithms in Rust
Language:Rust2 0
jdidion/IndexTools
IndexTools is a toolkit for extremely fast NGS analysis based on index files.
Language:Python2 0
jdidion/io-streams
Unbuffered and unlocked I/O streams
Language:Rust0 0
jdidion/jd-test-repo
A test repo
Language:Rust2 0
jdidion/leviosam2
Fast and accurate coordinate conversion between assemblies
Language:C++1 0
jdidion/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Language:Python2 0
jdidion/pytest-workflow
Configure workflow/pipeline tests using yaml files.
Language:Python0 0
jdidion/read-structure
Language:Rust1 0
jdidion/release-plz
Publish Rust crates from CI with a Release PR.
Language:Rust1 0
jdidion/seq_geom_parser
Testing out rust parsing of single-cell library geometry specifications
Language:Rust1 0
jdidion/streammd
Single-pass probabilistic duplicate marking of alignments with a Bloom filter.
Language:C++1 0
jdidion/syncmers
Library for finding syncmers from &[u8] in rust
Language:Rust1 0
jdidion/testing-proc-macros
Example of structuring a proc macro crate for testability
Language:Rust1 0
jdidion/tree-sitter
An incremental parsing system for programming tools
Language:Rust1 0
jdidion/tree-sitter-python
Python grammar for tree-sitter
Language:JavaScript1 0
jdidion/wdlTools
WDL tools for parsing, type-checking, and more
Language:Scala1 0