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v1.2.0
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@sof202 sof202 released this 08 Aug 15:12
· 75 commits to main since this release
v1.2.0
780bd0f
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sof202 Sam Fletcher
SSH Key Fingerprint: nykwyocG2cTDGTnL2DHjB2ckpLohO2TjU/LEIFuGVMg Learn about vigilant mode.

Features

  • Heatmap for partitioned heritability enrichment is now less crowded and instead shows ** or * for significance
  • Allow user to binarize bed and bam files (not just bam)
  • Added ability for user to specify the maximum number of iterations ChromHMM should use whilst learning models
  • Add an install packages script [for R]
  • Added warning message if the model with the optimum number of states has a higher BIC than the next (less complexity) model
  • The model with the optimum number of states will now be moved to the optimum states directory (so one only has to keep a single file)
  • Added a plot for isolation scores which can be used to help users decide what the threshold should be in Config.R

Refactors

  • Overhauled build process (config files)
  • Removed subsampling [and earlier] scripts (not really required and added a lot of complexity)
  • Removed preambles from top of shell scripts and updated usage to reflect this.
  • Removed 'checkpoint script' (no longer required due to subsampling stage being removed)
  • Output of RedundantStateChecker.R is more human readable now

Bug fixes

  • Fixed BIC and Likelihood plots not being created (bad file formatting)

Docs

  • Made necessary changes to reflect refactors and features
  • Removed config files from website (now outlined in README)
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