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