Janggu

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- Fixed typos in documentation

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- adapted pysam dependency
- fixed bug in coverage loading from BAM files

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- added predict_variant_effect as stand-alone function.
- adapted predict_variant_effect to accept a genome in fasta format in addition to the previously required Bioseq object.
- added idx argument input_attribution to allow the selection of the i^th sequence of a Bioseq object.

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- Added compatibility and tests for tensorflow 2.2.
- Adapted setup.py to enable the use with tensorflow 1.14 and tensorflow 2.2 and compatible keras versions, respectively.
- Expanded mode option for Cover.create_from_bed. New options: 'bedgraph', 'score_category' (synonym for 'categorical'), 'name_category'
- Fixed mode='categorical'/'score_category' behaviour for Cover.create_from_bed
- Mode 'bedgraph' enables compatibility with bedgraph format.
- Fixed issue with intervals overhanging the chromosome ends and intervals on non-existing chromosomes for Cover.create_from_bigwig and Cover.create_from_bam.
- Fixed issue in building DnaConv2D wrapper if the forward and revcomp layers were already built.

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- Improved JangguSequence which can be used with keras and tensorflow 2.0

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- Performance improvement for loading BED files.
- If no binsize is supplied, the binsize is detected automatically as the longest interval in the roi. Previously automatic detection was only offered if all intervals were of equal length, otherwise, a binsize needed to be specified manually.