Isotools

* added function to import samples from csv/gtf to import transcriptome reconstruction / quantification from other tools.
* dropped requirement for gtf files to be tabix indexed.

* fixed get_overlap - important for correct assignment of mono exonic genes to reference
* added parameter to control for minimal mapping quality in add_sample_from_bam. This allows for filtering out ambiguous reads, which have mapping quality of 0
* fixed plot_diff_result (Key error due to incorrect parsing of group names)
* New function estimate_tpm_threshold, to estimate the minimal abundance level of observable transcripts, given a sequencing depth.
* New function coordination_test, to test coordination of splicing events within a gene.
* Optional log or linear scale for the coverage axis in sashimi plots.

* added DIE test
* adjusted classification of novel exonic TSS/PAS to ISM
* improved assignment of reference genes in case of equal number of matching splice sites to several reference genes.
* added parameter to control for minimal exonic overlap to reference genes in add_sample_from_bam.
* changed computation of direct repeats. Added wobble and max_mm parameters.
* exposed parameters to end user in the add_qc_metrics function.
* added options for additional fields in gtf output
* improved options for graphical output with the command line script
* fixed plot_bar default color scheme

* fix: version information lost when pickeling reference.
* fix missing gene name
* added pt_size parameter to plot_embedding and plot_diff_results function
* added colors parameter to plotting functions
* various fixes of command line script run_isotools.py

* added command line script run_isotools.py
* added test data for unit tests

* Added unit tests
* Fixed bug in novel splicing subcategory assignment
* new feature: rarefaction analysis
* Changed filtering: expressions get evaluated during iteration
* Predefined filters are added automatically
* Add / remove filters one by one
* added optional progress bar to iter_genes/transcripts