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Releases: DEploid-dev/DEploid

v0.7-beta

18 Nov 01:09
c15dfb9
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v0.7-beta Pre-release
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DEploid-Bestpractice

Major improvement! Can handle thousands of haplotypes in the reference panel

  • New DEploid-Bestpractice pipeline:
    1. Use DEploid-Lasso to infer K,
    2. Fix K, use DEploid-IBD to infer proportions
    3. Fix K and p, use DEploid-Lasso to infer haplotypes

v0.6-beta.1

16 Oct 00:21
895e308
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v0.6-beta.1 Pre-release
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  • Apply -ibd flag at site with wsaf > 0 only

v0.6-beta

10 Oct 23:12
2f71665
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DEploid-Lasso

Use lasso algorithm to chose reference panel

  • New flags "-lasso" "-writePanel"

v0.5-release

18 Jan 22:50
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Updated documentation

v0.5-beta

13 Nov 13:48
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v0.5-beta Pre-release
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Improvement
Tuned parameters: sigma etc

Creating a time stamp for checking against

v0.4-release

10 May 15:34
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Major improvement

  • input scaling factor

New features:

  • parse threshold and window size to data explore
  • calculate diagnostics and show in log file

Bug fixed

  • forward and backward painting

v0.4-beta

25 Feb 16:41
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Major improvement:

  • Improved R interface
  • Use IBD method to infer proportions.
  • Use forward-backward posterior probabilities for painting

v0.3-release

24 Nov 08:16
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Improvements

  • R scripts syntax checked with lintr
  • Using its own random number generator for normal distributions. Results are not reproducible across platfomrs.

Bug fixed

  • R plotting wsaf across genome
  • path to utilities/dEploidTools.r is hardcoded
  • R wsaf histogram exclude momomophic sites

v0.3-beta.1

14 Oct 16:25
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Major improvements

  • R reading vcf header is no longer harder coded.
  • making changes to parsing parameters in order to accommodate the r interface.
  • Improved comments to the R code, with examples.

v0.3-beta

28 Aug 17:18
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Major changes and improvements:

  • Read compressed VCF
  • Output compressed VCF
  • Show progress when program is running
  • Improve document
  • Positions are stored as integers

Bug fixed:

  • No bug fixed in this version.