Custardpy

- Fixed a bug where ``juicer_map.sh`` failed when passing "\_" for ``fastq_post`` valuable and there were underscores (\_) in the FASTQ directory name.

- Added `libgit2-dev` to install `gert` in R
- Added a message in ``juicer_pigz.sh`` and ``juicer_unpigz.sh``

- Changed Python environment from conda to micromamba (`/opt/micromamba`)
- Updated Python from 3.8.17 to 3.10.13
- Install [HiCLift](https://github.com/XiaoTaoWang/HiCLift)

- Updated HiC1Dmetrics from v0.2.9 to v0.2.10
- Omitted `${juiceDir}/scripts/common/check.sh` which checks the number of ${outputdir}/merged_sort.txt, ${outputdir}/merged_nodups.txt, ${outputdir}/dups.txt and ${outputdir}/opt_dups.txt.

- Updated `distance_vs_count.Juicer` and `distance_vs_count.Juicer.log` to use minimum Q-value threshold of 30 and window size 50 kbp by default
- Updated `plot_distance_count.R` to set the background color to white
- Updated `plot_distance_count.log.R` to set the background color to white and limit the x- and y-axes
- Added `plot_distance_count_all.R`, `plot_distance_count_all.log.R`, `plot_distance_count_multi.R`, `plot_distance_count_multi.log.R`
- Modified `juicer_pigz.sh` and `juicer_unpigz.sh` to compress/uncompress aligned/dups.txt, aligned/opt_dups.txt and aligned/collisions*txt as well
- `makeEigen.sh`: Fixed the bug where the computation would not finish if the computation of PC1 in h1d failed.
- Fixed a bug where `pairtools` was not found.
- Added [CALDER2](https://github.com/CSOgroup/CALDER2)
- Updated chromap from v0.2.4 to v0.2.6
- Updated bedtools from v2.30.0 to v2.31.0

- 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.
- Updated HiC1Dmetrics from v0.2.5 to v0.2.9