version 2.0.0

2.0.0 (2024-5-22)

• Changed Python environment from conda to micromamba (/opt/micromamba)
• Updated Python from 3.8.17 to 3.10.13
• Install HiCLift

1.9.1 (2024-04-04)

• 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.

1.9.0 (2024-03-21)

• 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
• Updated chromap from v0.2.4 to v0.2.6
• Updated bedtools from v2.30.0 to v2.31.0