Changelog

Version - 1.3 - Inworks - 2022-12-11

Changed pipelines to use modisco-lite, old modisco will soon be removed
Added automatic shift scripts to repo and integrated with the pipeline
modisco now outputs both html and pdf. pdf can be shared with anyone.
Use ATAC, DNASE not ATAC_PE, DNASE_SE anymore
Simplyfing workflows to include only two main workflows, chrombpnet_train_tf_model, chrombpnet_train_bias_model
Restructuring README, moving tutorial to additional documentation and introducing FAQ, and only two pipelines (chrombpnet_train_tf_model, chrombpnet_train_bias_model)

Typo fix - (PR#31-36)
We can now specify ylimit in marginal footprinting plots (PR#27)
PR#30 merged to do fast genome wide gc binning and bug fix to ensure case-sensitve GC calculation. Adds a unit test to make checks.

Marginal footprinting no longer hardcoded to take only chr1, it now inputs the fold json. (PR#20)
Invivo footprinting is made compatible with the new input repo changes. (PR#22)
Pandas read bugs fixed for gc-matching scripts. (PR#15)
Tutorial now exits when one part of the pipeline breaks instead of proceeding further. (PR#18)
Added the fast binning scripts at src/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets (PR#11)
Added pseudocount in metrics.py (PR#13) - needs further review.

Seed setting fixed for training. Seed was set improperly - preventing shuffling for every epoch. (PR#19)
return coordinates while training for debugging - returns status of the point such as revcomp,peak/nonpeak,coordinates etc

In step6_train_chrombpnet_model changed the file saving name bug
Changed scripts in src/evaluatuion/make_bigwigs/ to be compatible with new dir structure

Added a note in README that users can continue to use the pre-trained bias model from chrombpnet-lite repo, if thats what they have been using till now
Changed the default modisco crop setting in tutorial from 1000 to 500
Fixed a bug in src/evaluation/modisco/run_modisco.py in directory creation