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Commits on Dec 6, 2018

• [README] Edit README to include pipeline instructions; version v0.8.12

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Commits on Nov 15, 2018

• [notebooks] Add HiC-linksize-empirical-distribution

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• [extract] Fix crashes when link size exceeds MaxLinkDist

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Commits on Nov 14, 2018

• [partition] Fix issue #1, use --minREs strictly as user input

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• [extract] Extract first part of the sequence name

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• [evaluate] Update MaxHalford/gago => MaxHalford/eaopt

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Commits on Sep 5, 2018

• [README] Add partition cmd on pruned output

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• [partition] Add partitionFlags

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Commits on Sep 4, 2018

• [cluster] Make passRatio a bit more stringent

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• [partition] Change default MinREs

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• [prune] Summary statistics of pruned links

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• [prune] Update score in prune

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• [prune] Replace *AlleleGroup with groupID

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• [prune] Add pruneCrossAllelic()

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• [prune] Add writePairsFile()

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Commits on Sep 3, 2018

• [extract] Add label column to pairs.txt

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• [prune] Add parseAllelesTable()

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Commits on Sep 2, 2018

• [prune] Add prune.v2.cpp

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• [evaluate] Revert back to EvaluateSumRecip() as default Evaluate()

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Commits on Jul 28, 2018

• [cluster] Update N => nNonSkipped

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Commits on Jul 26, 2018

• [partition] Add 1 pseudocount to RE counts; Also lower the MinRE cutoff

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Commits on Jul 22, 2018

• [release] Add packr to goreleaser

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• [build] Add mergeTours()

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• [cmd] Add pipeline

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Commits on Jul 19, 2018

• [plot] Use packr to distribution html

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• [plot] Add overflow

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Commits on Jul 8, 2018

• [optimize] Reuse rng

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• [clm] Do not read header

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• [tests] Update functional-tests.sh

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• [tests] Clean up contents in tests

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Commits on Jul 7, 2018

• [images] Add allhic-plot-s

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• [optimize] Simplify optimize interface

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• [plot] Add X-axis label

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• [plot] Isolate relevant code from anchor to go

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• [plot] Add plot.go

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