version 1.8.0

1.8.0 (2024-03-03)

• 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.