Releases: tanghaibao/allhic
v0.9.13
d0ed869
tanghaibao
Haibao Tang
v0.9.12
v0.9.8
[goreleaser] Release v0.9.8
v0.8.12
Changelog
84f89f7 [README] Edit README to include pipeline instructions; version v0.8.12
04531ca [notebooks] Add HiC-linksize-empirical-distribution
bf822fb [extract] Fix crashes when link size exceeds MaxLinkDist
a301323 [partition] Fix issue #1, use --minREs strictly as user input
d9eb5b7 [extract] Extract first part of the sequence name
f0a075e [evaluate] Update MaxHalford/gago => MaxHalford/eaopt
f2f9392 [README] Add partition cmd on pruned output
8185b0a [partition] Add partitionFlags
4d7935d [cluster] Make passRatio a bit more stringent
a0cf7d3 [partition] Change default MinREs
bdc30e7 [prune] Summary statistics of pruned links
831f901 [prune] Update score in prune
dba743f [prune] Replace *AlleleGroup with groupID
7d66dbe [prune] Add pruneCrossAllelic()
1d9e0ce [prune] Add writePairsFile()
c36c4f4 [extract] Add label column to pairs.txt
c42f43a [prune] Add parseAllelesTable()
d660177 [prune] Add prune.v2.cpp
afd492a [evaluate] Revert back to EvaluateSumRecip() as default Evaluate()
8ed9616 [cluster] Update N => nNonSkipped
ddf6835 [partition] Add 1 pseudocount to RE counts; Also lower the MinRE cutoff
51110c2 [release] Add packr to goreleaser
v0.8.4
Changelog
16de042 [build] Add mergeTours()
7cf2674 [cmd] Add pipeline
e6c66e9 [plot] Use packr to distribution html
b8e5e26 [plot] Add overflow
a44064e [optimize] Reuse rng
3a2373d [clm] Do not read header
66e80e0 [tests] Update functional-tests.sh
8c518a5 [tests] Clean up contents in tests
ed5959a [images] Add allhic-plot-s
e16bbfa [optimize] Simplify optimize interface
82abd1b [plot] Add X-axis label
19a4dc6 [plot] Isolate relevant code from anchor to go
6418179 [plot] Add plot.go
88641ed [plot] Fix dimensions of the plot
9100381 [plot] Implement heatmap
a1cafed [plot] Add plot.html
efc52af [optimize] Add parseClustersFile
06b5ab9 [partition] Do not run clustering when k = 1
8b23329 [model] Add LinkDensityModel and reduce dup code in assess and extract
8761a30 [README] Edit README to remove old doc
ebb6c39 [cluster] Write partitions to file
b27bb47 [build] Speed up build
ac14455 [build] Add parseAllTours() back
0abaa4f [README] Update doc on build
0d0f3d1 [partition] Simplify Run()
29c9530 [extract] Normalize output file names
aeae14a [extract] Remove MLE calculation
3e2621f [cluster] Recover skipped contig
a461f93 [cluster] Add clusters to Partitioner
f3d6c8d [cluster] Add printClusters()
8a8d3a5 [extract] Add bam flags
e576250 [cluster] Skip contigs during clustering
3bae32a [partition] Fix bug in skipRepeats()
ed2f50d [partition] Store ai, bi in ContigPair
438a8bd [partition] Add skipRepeats()
ba98d9a [extract] Export limited number of fields in ContigPair
e7d16b7 [extract] Fix position bug
ba11153 [extract] Simplify contig info
c4cfd19 [extract] Start unifying int64 for genome coordinates
e4ba144 [partition] Add skipContigsWithFewREs()
01bde3b [extract] Export RE counts to file
92c9f7b [cluster] Replace list with slice
947dfd3 [notebooks] Add two notebooks
961532a [anchor] Skip contigs in imported path that are not found
5e2f2fb [anchor] Add --tour to dump matrix for existing path
b7bce45 [anchor] Write to tour file
18668e7 [optimize] Add resume capability
9c50fbb [anchor] Experimental export of intermediate path
4123920 [graph] Make ties to make the algorithm more stable
9cc9ada [orientation] Use SumLog in EvaluateQ()
a2f34a3 [evaluate] Add MutPermute and MutSplice
aaf1000 [cmd] Remove crossrate
86b2838 [evaluate] Use MaxHalford/gago
4d6e7ee [assess] Use power law in caluclation in computeLikelihood()
a9bf4e6 [evaluate] Use rng in randomTwoInts
a0cefdf [evaluate] Simplify mutation random calls
f8b0fb6 [evaluate] Test 2.5Mb LIMIT
d145313 [cmd] Add command line options to optimize
c15bcbe [evaluate] Change LIMIT to 5Mb
b5105b7 [evaluate] Add LIMIT back in the Evaluate()
e76e9c8 [evaluate] Set maxscore initially to minfloat
b56b6e3 [evaluate] Use the Evaluate() function based on log(dist)
13917c6 [assess] Disable Println() in assess
eda4da4 [assess] Add fixPowerLaw()
91a5e8c [anchor] Add getL50()
f158333 [anchor] Add flanksize
b60928c [anchor] Add flanksize to bisect()
fcf1020 [anchor] Add serialization code of Anchorer
e93a185 [anchor] Add makePath()
3067d5c [anchor] Add iterativeGraphMerge()
d9e7f50 [anchor] Add findCountCutoff()
d74afcf [anchor] Remove scoreTriangle()
29fddc2 [anchor] Add Piler to search number of overlapping intervals
14020a4 [anchor] Use int64 instead of float64
b708816 [anchor] Add convenience Node.length() function
d820453 [anchor] Add inspectGaps()
4142516 [anchor] Add identifyGap()
8157ef9 [anchor] Fix secondLargest
48e2ab5 [anchor] Track PathSet
36eff4f [anchor] Still buggy graphRemake
159de19 [anchor] Simplify LNode and RNode
79db2a7 [anchor] Do not modify graph when making confidence graph
dade67c [anchor] Remove Registry
b599c16 [anchor] Simplify logging messages
3b8187c [anchor] Simplify orientation
f4e8c28 [anchor] Add splitPath()
41006e0 [anchor] Stopping merging until 1 path
3a9b5c8 [anchor] Add getUniquePaths()
9401600 [anchor] Add printPaths()
1a4926e [graph] Fix path counting
6e0a1f9 [anchor] Replace Path with *Path
4246deb [graph] Ignore intra links
979e42b [anchor] Fix bug in the center contig
67b3982 [anchor] paths[i].bisect() now working
8347afa [anchor] Simplify dfs logic
1c635b9 [anchor] Add iterative merges (not working yet)
356427f [cmd] Add Xingtan to author list
5b9db17 [assess] Update cutoff to be 0.95
c321dfa [assess] Write prob to file
7e28830 [assess] Calculate post. prob. from log likelihood
d916934 [assess] Normalize probability per bin size
3e3e9af [assess] Add ComputePosteriorProb()
572509a [assess] Add MakeProbDist()
4549ee3 [assess] Read intra- and inter- contig links
12aed00 [assess] Add ReadBed()
6872a1e [scripts] Add tour2asm.pl and prune-all-new.cpp
e1cbfba [assess] Add extraction of intra-contig links
0d052b2 [assess] Ass assess.go
385f539 [graph] Reverse negative oriented path
79d7829 [anchor] Change orientations to be {-1, 1}
5a5e093 [base] Use math.MinInt32
2c5780b [graph] Add breakCycle()
13c2860 [graph] Store edge weights in path
7247f73 [graph] Implement generatePathAndCycle()
ddf4857 [graph] Add confidenceGraph
6ec2ee6 [graph] Build confidence graph
d51bfe2 [graph] Add graph.go
2a65631 [anchor] Add anchor.go
c96868e [anchor] Handle reverse oriented contigs in Path
df1e9e0 [anchor] Instantiate edges in anchor
7d39921 [anchor] Update registry after bisect()
cda29d5 [anchor] Change int to *Contig in struct Path
582888a [anchor] Add bisect
0824320 [anchor] Add anchor.go
v0.8.2
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
Automated with GoReleaser
Built with go version go1.9.2 darwin/amd64