Isotools

* fixing 8: AssertationError when unifying TSS/PAS between transcript
* improved domain plots: ORF start and end do not appear like exon exon boundaries.
* API change: separated ORF prediction from QC metrics calculation.
* new feature: count number of upstream start codons in Gene.add_orfs() (called by default when adding QC metrics to transcriptome)
* new feature: calculate Fickett testcode and hexamer score for longest ORFs, to separate coding and noncoding genes.

* fixed bug in filter_ref_transcripts with no query
* export gtf with long read transcripts as well uncovered as reference transcripts
* fix warning in plot_diff_results
* changed export to rMATS: events report complete flanking exons of top covered isoform
* fixed bug with transcript_id_col parameter in add_sample_from_csv
* fixed handling of interpro protein domains
* improved documentation: syntax highlighting, code style, additional explanations on filtering

* restructured tutorials
* new feature: add domains to differential splicing result tables.
* new feature: min_coverage and max_coverage for iter_genes function.

* new feature: add protein domains from 3 different sources and depict them with Gene.plot_domains()
* new feature: restrict gene and transcript iterators on list of genes of interest
* new feature: filter_transcripts function for genes
* changed SUBSTANTIAL filter to 1% of the genes total (was 5%)
* coordination test:
* changed argument and column naming, to make it consistent with other test results
* added conditional delta PSI effect size measure
* order of events is now according to gene strand: A upstream of B

* new feature: find longest ORF and infer NMD of lr transcripts (and annotation)
* new feature: allow for several TSS/PAS per intron chain and unify them across intron chains
* changed default parameter of filter_query in run_isotools script to "FSM or not (INTERNAL_PRIMING or RTTS)"

* bugfix: KeyError during transcriptome reconstruction in _add_chimeric.
* bugfix: default colors in plot_diff_results.