Bug Fixes
* Fix gtf.tail() (158).
* Fix merge_attr (147).
* Fixed merged statistics calculation in *ologram_merge_runs*.
* Fixed memory leaks in OLOGRAM's multiprocessing. RAM usage should decrease by 25-70% in certain cases.
* Fixed a bug where OLOGRAM would needlessly store empty lists if certain combinations were not encountered.
* Fixed several bugs in OLOGRAM that could result in dead process hanging indefinitely, including a histgram drawing bug.
* OLOGRAM now merges consecutive intersections, to prevent a bug that resulted in double countings.
* Fixed a bug in OLOGRAM where files with less than 2 regions were needlessly discarded.
API/CLI Changes
* OLOGRAM will now also produce separate histograms for each combination length.
* The --chrom-file argument now accepts "mm8_ens", "mm9_ens", "mm10_ens", "hg19_ens", "hg38_ens", "rn3_ens" and "rn4_ens" which correspond to internal chromosome info files in ensembl format (i.e. no 'chr' prefix) (146).
* OLOGRAM has two new arguments (--hide-undef and --pval-threshold) to hide undefine or high p-values.
* ologram_modl_treeify has a new argument (--min-inheritance) to add combinations only if they represent a given proportion of an existing parent.
* In OLOGRAM-MODL, whether to use exact combinations or not (should A+B+C count as an observation of A+B ? Yes if not exact) is now controlled by an argument (--exact).
* Added an argument to OLOGRAM to hide bars with undefined p-values (149).
Code changes
* Minor optimizations to overlap computing.
* pygtftk now requires Python >=3.8, <3.9.
* Major optimizations to OLOGRAM's handling of RAM using newly-created structures.
* Reduced OLOGRAM time cost by removing operations (computation of relative combination exactitude) that were not needed.
* OLOGRAM's statistics computation with multiprocessing now uses a batch system instead of individual jobs.
New Features
* OLOGRAM now has an argument to determine if certain sets within --more-beds should be kept intact during the shuffling.
* The get_attr_value_list command now accepts -k '*'.