4.1 - Full release

What's Changed

Made some mostly minor changes and several bugfixes. Please post any lingering issues after re-trying with NEAT 4.1

• updating test config by @joshfactorial in #79
• Updates to README by @joshfactorial in #81
• Update ChangeLog.md by @joshfactorial in #82
• Removing pybedtools dependency. by @keshav-gandhi in #84
• Vcf test by @joshfactorial in #86
• Updated descriptions of the commands and small edits! by @keshav-gandhi in #90
• Feature/fixing coverage by @joshfactorial in #95
• Update README.md by @joshfactorial in #96
• Added functionality for save trinucleotide by @keshav-gandhi in #92
• Found a merge conflict by @joshfactorial in #98
• Minor changes to output_file_writer by @keshav-gandhi in #99

Full Changelog: 4.0...4.1

v4.0-beta.2

This release represents a major shift in NEAT. Please feel free to ask questions. NEAT 3 is still available under releases if prefer to use that in your workflow.

UPDATE 11/17/2023

A few issues have come up and this release should be considered unstable. We hope to stabilize NEAT in version 4.1 with some current changes in dev. Feel free to try the dev branch or the current repo, or use NEAT 3.4 until 4.1 is released.

v3.4

This version of NEAT 3 includes some extra help messages.

v4.0-beta

This release represents our newest version of NEAT. In this beta release, the functional capabilities are:

• Create a vcf of random mutations (can include an input list of mutations)
• Create a mutated fasta file (apply mutations to fasta)
• Generate reads in a fastq. This applies the above mutations and random sequencing errors to depth of coverage specified by user
• More robust error and debugging messages
• pip installable - please see README for instructions.

Things we have yet to implement:

• Bam creation - The framework is in place, and we expect this to be done soon
• Model generation - the current model creation scripts require update to the new format. For now, you will only be able to use default models (except the config-level parameters, like coverage, fragment length and standard deviation, etc)
• Complex variants - much of the framework is in place for complex variants, but not yet implemented. We can apply large variants that are input from a vcf, provided they are done in a simple ref/alt format (AAGAGA/TTC). We cannot handle, yet, CNVs are variants with non-standard notation.
• Parallelization - We are underway implementing parallelizing NEAT's read generation processing, but have not yet implemented it
• Other bells and whistles - Some may work, some may not depending on where they fall in the code.
• Command line interface - We are working on a reverse-compatible CLI for NEAT that will allow implementation of NEAT with minimal changes on the user side, for existing pipelines.

Items we seek from users:

• Patience - please review the README for the latest installation procedures and expect NEAT 4.0-beta to be a work-in-progress
• If you do not need a BAM file, please try NEAT 4.0 and provide any feedback you have on the new tool
• Bug reports - It will be very helpful to include the full log from the NEAT run and the input config, so we can reproduce any errors and track down their source
• Suggestions for improvements - We've tried our best to implement NEAT in a new way that should ultimately be faster and more flexible; however, we would like to hear feedback on things that don't work as well, slowdowns, data problems, in addition to feedback on the new features that you liked.

What's Changed

• Feature/modularization by @joshfactorial in #63

Full Changelog: 3.3...4.0-beta

SPECIAL THANKS

Contributers:

• @YashWasnik7
• @keshav-gandhi
• @Ralhazmy1
• @VarenyaJ
• @amir-kazemi

v3.3 - final version 3

This is the final version of NEAT 3.0 that will be released. Future work will be focused on NEAT 4.0. Please continue to use NEAT 3.2 for full feature capability and continue offering suggestions and comments.

NEAT v3.2

After 3.1 had to be walked back for bugs, the new and improved NEAT version 3.2 should clean up a lot of lingering issues.

What's Changed

• Paired reads orientation generation behavior by @MeatKatlet in #24
• Fixes to the Poisson distribution that was sampling for number of mut… by @joshfactorial in #43
• removing debug print statements by @jkalleberg in #42
• Resolved #39 by @jkalleberg in #41

New Contributors

• @MeatKatlet made their first contribution in #24
• @jkalleberg made their first contribution in #42

Full Changelog: 3.0...3.2