hickit-0.1.1

Code used to generate the final results in Tan et al. Nat Struct Mol Biol (2019), which can be acquired from GSE121791.

Updates:

• Added #unit line in the header of .3dg files, indicating how many "particle radii" one unit length equals to. In nuc_dynamics (and therefore dip-c), the particle radius is defined such that the ideal backbone distance between two adjacent beads is 1.0 radius, and that the repulsion distance between beads is 2.0 radii.
• Added -M option to skip merging adjacent beads during 3D modeling, for compatibility with nuc_dynamics and dip-c. With -M, each bead will have the same genomic length (for example, 20 kb).
• When merging duplicates, merge their phases too.
• Added --all-close-leg option to remove all close-legged contacts regardless of strands.
• Added --val-radius option to flag close contacts during imputation.
• Added --dbg-val option for debugging during imputation.
• Can read files with #chromsize rather than #chromosome in the header, for compatibility with the pairs format.
• Fixed typos in README, especially regarding the pseudoautosomal regions (PARs).
• Other minor bug fixes.

hickit-0.1 (r275)

Initial release. Code used to generate the final hickit results in Tan et al (2018), which can be acquired from GSE117876, as well as from the v0.1 release page.