Isonform

Changed the name and structure of the isON pipeline. full_pipeline.sh was removed as now the isON_pipeline.sh has a better usage interface and is easier to use with pip installations. Additionally changed the file type of isONform_parallel and main.

Solved the recursion depth bug that was still encountered in version 0.2.0, removed the command line argument --use_racon as isONform does not support the parameter.

This release improves the runtime and overall performance of the isONform algorithm wrt. to version 0.1.0. while slightly changing the results of the algorithm.
The following points have changed over version 0.1.0:

- Usage of more efficient data structures, removal of unnecessary code chunks, restructuring of the repository.
- Changes in the cycle detection during the generation of the graph
- Improvements of the minimizer calling by using new rules : 1. sample last minimizer if ties and 2. do not resample a minimizer if last minimizer is still in the window. Reduces repetitive anchors a lot in poly-regions. This improves runtime for instances where long ploy regions are frequent.
- Adding an upper limit on how repetitive a paired-minimizer anchor can be in the data. If the anchor is too abundant the respective anchor pair is not used for the graph generation.
- Changes to arguments needed to run the isONform algorithm. (removed the usage of --slow, --merge_sub_isoforms_3, --merge_sub_isoforms_5, while adding the arguments --tmpdir [used if the temporary directory generated by isONform by default is not usable] and --clustered [used for data that does not require correction, e.g. Pacbio data]).

This is the version of isONform that was used for all analyses indicated in the paper version submitted to ISMB.