Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
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
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
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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