Releases: lh3/hickit
Releases · lh3/hickit
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.