Release v4.0-beta · ncsa/NEAT

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

Full Changelog: 3.3...4.0-beta

Contributers: