Tobias

- Fixed error in parsing "patterns" for DownloadData
- Fixed errors for reading/writing bigwigs when pybigwig.numpy == 0
- Improved exceptions for bigwig/bam reading/writing

- Removed 'gimmemotifs' from requirements and included check in MotifClust (only tool needing gimmemotifs) instead. This is a temporary hack solving various install/conda issues.
- Fixed smaller bug in bigwig writer for one-region output
- Added check for samtools in SubsampleBam
- Added PG-line to FilterFragments output bam
- Added interactive html plots with motifs to BINDetect
- Adding --smooth function to PlotAggregate
- Fixed bug with overlapping figure labels in PlotAggregate
- Added .pickle output of ATACorrect bias object to use in other applications
- Fixed bugs in PlotTracks due to svist4get update; pinned =1.2.22 to setup.py
- Split internal structure of package into tools/utils/scripts
- Fixed bug in BINDetect cutting off last column of _bound/_unbound files.
- Added --naming to BINDetect
- Added DownloadData tool to enable download of test_data/ directory from s3
- Changed default --outdir's to be <toolname>_output
- Fixed one-off error in MaxPos
- Updated README with links to wiki
- Additional bugfixes

- Fixed error reading parser and fonts for PlotTracks
- Restructure of motifclust-functions to be included in OneMotif and MotifList classes
- Smaller bugfixes

- Added ClusterMotifs and FilterFragments to tools
- Restructured backend organization of parsers to speed up commandline 'TOBIAS'

- Added PlotTracks to tools
- Fixed smaller bug with flank estimation in footprint calculation
- Fixed rescale to original sum in ATACorrect
- Added option to exclude outliers from aggregate plots

- Added CreateNetwork to tools
- Smaller bugfixes