Develop#265

Merged

joshfactorial merged 103 commits into

mainfrom

May 3, 2026

Commits on Oct 4, 2025

Commits on Nov 12, 2025

Updated script to include paired-ended runs
karenhx2
committed

Commits on Nov 29, 2025

Commits on Dec 5, 2025

Commits on Dec 18, 2025

Implemented CLI for wrapper
karenhx2
committed

Commits on Jan 26, 2026

Removed extra copy of runner code
karenhx2
committed

Commits on Jan 29, 2026

Commits on Jan 30, 2026

Renaming to parallel_block_size and parallel_mode; fixing tests.
keshav-gandhi
committed

Commits on Feb 1, 2026

Fixed bugs with config files and output stitching
karenhx2
committed

Commits on Feb 2, 2026

Installation instructions.
keshav-gandhi
committed

Commits on Feb 4, 2026

Merge branch 'develop' into feature/karen_bacterial_wrapper
joshfactorial
authored

Commits on Feb 12, 2026

Commits on Feb 18, 2026

Merge pull request #240 from ncsa/quality-of-life
keshav-gandhi
authored

Commits on Feb 22, 2026

Merge branch 'develop' of github.com:ncsa/NEAT into feature/karen_bacterial_wrapper
karenhx2
committed

Commits on Feb 23, 2026

Markov quality score model changes copied in here.
keshav-gandhi
committed

Commits on Feb 26, 2026

Merge branch 'develop' of github.com:ncsa/NEAT into feature/karen_bacterial_wrapper
karenhx2
committed
Updated wrapper
karenhx2
committed
Developed script for wrapping bacterial chromosomes

karenhx2
authored and
joshfactorial
committed
Cleaned up files

karenhx2
authored and
joshfactorial
committed
Worked on testing functions for stitching outputs together

karenhx2
authored and
joshfactorial
committed
Removed reference and data files

karenhx2
authored and
joshfactorial
committed
Updated script to include paired-ended runs

karenhx2
authored and
joshfactorial
committed
Implemented CLI for wrapper

karenhx2
authored and
joshfactorial
committed
Removed extra copy of runner code

karenhx2
authored and
joshfactorial
committed
Fixed bugs with config files and output stitching

karenhx2
authored and
joshfactorial
committed
Finished final debugging

karenhx2
authored and
joshfactorial
committed
Accidentally removed poetry file and re-adding it

karenhx2
authored and
joshfactorial
committed
Updated wrapper

karenhx2
authored and
joshfactorial
committed
A couple of changes related to filetypes
joshfactorial
committed
Fixing a small error introduced by merging
joshfactorial
committed
Resolved merging conflicts
karenhx2
committed

Commits on Feb 27, 2026

README updates including Markov stuff.
keshav-gandhi
committed

Commits on Feb 28, 2026

Removing accidental log file.
keshav-gandhi
committed

Commits on Mar 5, 2026

Commits on Mar 25, 2026

merge conflict resolution
joshfactorial
committed

Commits on Mar 28, 2026

Commits on Apr 4, 2026

updating tests
joshfactorial
committed

Commits on Apr 5, 2026

Commits on Apr 7, 2026

Commits on Apr 8, 2026

Merge branch 'develop' into feature/karen_bacterial_wrapper
joshfactorial
committed

Commits on Apr 10, 2026

Commits on Apr 18, 2026

Commits on Apr 26, 2026

Solving VCF-related issues.
keshav-gandhi
committed

Commits on Apr 27, 2026

Commits on Apr 28, 2026

Revised README for NEAT 4.4.
keshav-gandhi
authored

Commits on Apr 29, 2026

Add Markov quality model test coverage and fix invalid test data

joshfactorial
and
claude
committed

Commits on Apr 30, 2026

Merge pull request #269 from ncsa/update-readme
joshfactorial
authored

Commits on May 1, 2026