Spladder

Bugfix release addressing issue 78.

This is the first release of SplAdder using Python 3. In addition to improved testing and the correction of minor bugs, we have re-designed the user interface. Following, we provide a list of the most notable changes:

* SplAdder now uses sub-commands. The previous scripts for graph building, visualization and testing have been replaced through three modes: `build`, `viz` and `test`
* the dash (`-`) is now consistently used in all parameters (e.g., `--merge_strat` has now become `--merge-strat`)
* binary flags have been re-introduced and can be directly switched on or off without an additional argument (e.g., `--verbose y` has become `--verbose` and `--primary-only n` has become `--no-primary-only`)
* `-T` has been replaced by `--extract-ase`

We also made some additional changes:
* SplAdder can now be installed via `pip`
* the concept of replicates was not used for the `build` phase and has been removed from the code
* the Matlab code has been removed
* additional test cases have been introduced and test coverage was increased
* some new settings previously only accessibly through changes in the code have been made available to the user
* the code has been cleaned up further

Fixing issue with `spladder` entry point.

This version is the legacy release for SplAdder running under Python 2.7.

It has the following changes relative to the last release:
* change of entry point, so it can be installed using pip
* addition of end to end test testable with pytest
* several bug fixes

This release contains quite some improvements and bug fixes:
* improved filtering of overlapping genes (this now happens on individual junction level)
* introduced filtering option for detection of events (e.g., edge limit per gene)
* adapted structure of hdf5 files
* improved the diagnose plots for differential analysis
* added robustness when handing various input file formats
* add PSI information into the pipeline
* improved filter criteria for exon skipping events
* allow for capping the gene expression variability in differential testing to remove extreme outliers
* when making events unique over inner coordinates, the shortest version is kept (instead of the longest)
* allow for compression of BAM files into sparse representation

This version is the first official release of SplAdder. It contains an improved bam caching and parallelization. As some of the output files are named differently, it will not work on project directories created with previous versions.