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@tanghaibao tanghaibao released this 28 Jan 05:44
· 243 commits to main since this release
v0.8.2
20241d6

Changelog

20241d6 [allhic] v0.8.2
da04b15 [CI] Add several test files
0dbf637 [CI] ADD .goreleaser.yml
95ec665 [partition] Remove redundant edges
53cc240 [partition] Print out contig names
b0ca368 [partition] Output all partitions
250104f [partition] Code dup in NewmanSubPartition
c82f012 [partition] Continue onto sub-partitions
01f9a5b [partition] Do not check visited
2528d3d [partition] Speed up calculation of Q
579e667 [partition] Parallel refinement
a98e08f [partition] Alert if cannot be further divided
9cc78b9 [partition] Add RefinePartition()
ddb5968 [partition] Add eigen decomposition in go
d618fb9 [partition] Generate adjacency matrix
aca84e4 [partition] Read graph in go
3f0cba8 [partition] Print out partition
5b900d6 [partition] Write edge list
97d88b3 [partition] Add help string for newman_modularity.py
95e7ba5 [partition] Fix fine-tuning method
26d26fb [partition] Fine-tuning in newman_modularity
70e4306 [partition] Implement newman_modularity.py
b036a60 [partition] Add Newman modularity Python prototype
0a99d5d [partition] Implement CountLinks()
870c576 [README] Update installation cmd
051ef0d [allhic] Replace docopt with clil
d4fb474 [allhic] Iteratively run pruneByDensity()
8cddb35 [allhic] Fix issue with Scanner() not having enough buffer
98ed3ce [allhic] Print FLIPALL log
4f13b24 [allhic] Add --mutpb and --cxpb in cmd/allhic
31dc3ca [allhic] Add crossRate in GARun()
597e1fa Merge branch 'master' of github.com:tanghaibao/allhic
cf8477b [CI] Add gif in README
87989d3 [allhic] Make a copy before sort in median()
6fe21e7 [allhic] Sort first in median()
c44633e [allhic] Print invalid tigs in clm
897e326 [allhic] Merge Version into base
ce0e69f [CI] Install package in the root dir
c0f9078 [CI] Add travis badge in README
b4cecaa [allhic] Log GARun intermediate results
2430328 [CI] Add command in README
b3e980a [allhic] Add flipOne in orientation
dd2f0be [allhic] Add flipWhole()
e6f8a7e [allhic] Pass options into optimize
599ee26 [allhic] Add command-specific docopt
5703c1a [CI] Add .travis.yml and functional tests
93ed0b2 [allhic] Generate Q matrix
2403821 [allhic] Perform eigh on matrix O
4a20532 [allhic] Add orientation.go
65cb039 [allhic] Write tour to tour file
f6237ac [allhic] Implement pruneTour()
77cd16a [allhic] Add pruneTour()
c85fac0 [allhic] Add pruneBySize() in clm
0f0cdd0 [allhic] Add pruneByDensities() in clm
b8e3f05 [allhic] Use a lighter struct for GA
7787bfb [allhic] Simplify data structures in clm
498e830 [allhic] Simplify data structures in clm
100301a [allhic] Use +/- directly as sign
52deeb2 [allhic] Stores orientations in map
f50a3c9 [allhic] Add GoldenArray()
e79d34a [allhic] Parameterize GA setup
c8bdc85 [allhic] Set convergence criteria
76b9b8a [allhic] Expose population settings
d6b0126 [allhic] Use genome mutation in evaluate()
a6a9f7c [allhic] Implements GARun()
e493349 [allhic] Implements gago.Genome interface
e60eb10 [allhic] Implement Slice interface in evaluate
cae47c1 [allhic] Make a struct to hold the tour
db97a79 [allhic] Shuffle array for different score
da6f3ef [allhic] Generate default tour in Activate()
0d82d5c [allhic] Add clm.M()
982f002 [allhic] Use logging in partition
f8bba7e [allhic] Add allhic/optimize.go
8b23082 [allhic] Fixed logger
fac9ca0 [allhic] Add ParseClm() in allhic/clm
c33d5de [allhic] Add allhic/clm.go
9ba4e49 [allhic] Add partition.go
82a6ee8 [allhic] Add dir structure
0e1a535 [allhic] Move all nim code into nim folder
ce13e7d [partition] Print contact matrix to file
5da063d [partition] Use result variable in count_links()
6ca2441 [partition] Simplify tig to id conversion
de6fe8a [partition] Update matrix entries in contact matrix
0c9cbea [partition] Compile number of links in a matrix
06200c0 [partition] Sort reads by name
f0ffa16 [allhic] Add count_links() in hic/partition
91f248f [allhic] Add hic/partition
4a03efc [allhic] Add docopt
137f31f [CI] Rename hic_opt to allhic
527cfff [hic] Implement score_evaluate()
5d7570d [hic] Add cumSum()
95869e0 [hic] Add matrix.nim
66c0bca [hic] Prune small contigs
49d8406 [hic] Add report_active()
cdf113b [hic] Implement hic.clm.parse_clm()
b040c3e [hic] Add hic.clm.parse_clm()
4317cf8 [hic] Read tig sizes into a table
a078abc [hic] Implement hic.clm.parse_ids()
6755bc9 [hic_opt] Initial commit
189535e Initial commit

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