Custardpy

- Major Update: If you experience any problems with this version, try the previous version (v1.7.2) and compare the results. If the problem persists, please report it to GitHub issues.
- The scripts in `juicer/scripts/common` used in Juicer were replaced to the original C codes and the computational time of Juicer is dramatically improved.
- Replaced `chimeric_blacklist.awk` with `Juicer_chimeric_blacklist`
- Replaced `dups.awk` with `Juicer_remove_duplicate`
- Replaced `fragment.pl` with `Juicer_fragment`
- Replaced `statistics.pl` with `Juicer_statistics`
- During this improvement I found a bug in `chimeric_blacklist.awk` where the names of non-autosomes (e.g. chrX and chrY) were not distinguished. This bug has been fixed in the new `Juicer_chimeric_blacklist`.
- This bug seems to be related to the new version of Juicer, which uses the chromosome names chr1,chr2,chr3, not 1,2,3. I have confirmed that the output of `Juicer_chimeric_blacklist` is identical to the older Juicer.
- Added the Jupyter notebooks for the CustardPy API in the `tutorial/` directory.
- Added the notebooks to the Manual.

- Modified `gethg38genome.sh` and `getmm39genome.sh` to also create the genometable file.
- Bug fix in samtools installation
- Updated SAMtools from 1.17 to 1.19.2
- Updated SRAtoolkit from 3.0.2 to 3.0.10
- Change WORKDIR from /opt to /home/ubuntu
- Installed `sudo`

- Modified `gethg38genome.sh` and `getmm39genome.sh` to also download the refFlat data.

- Fixed the bug in `plotHiCfeature` where TADs and loops were not being rendered
- Removed the restriction site directories of Juicer and Cooler from this repository to reduce the size
- Added `generate_binlist_from_gtfile.py` for 3DChromatin_ReplicateQC analysis
- Added `07.QualityCheck.sh` in `tutorial/Hi-C`

- Added [Mustache](https://github.com/ay-lab/mustache)
- Added [Chromosight](https://github.com/koszullab/chromosight)
- Update Hi-C Tutorial that uses [Nakato et al.,s RPE cells](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196034) for the example data

- AluI restriction enzyme for BAT Hi-C added to Juicer and Cooler