v0.7-beta

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

• Apply -ibd flag at site with wsaf > 0 only

v0.6-beta

DEploid-Lasso

Use lasso algorithm to chose reference panel

• New flags "-lasso" "-writePanel"

v0.5-release

Updated documentation

v0.5-beta

Improvement
Tuned parameters: sigma etc

Creating a time stamp for checking against

v0.4-release

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

Major improvement:

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

v0.3-release

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

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

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.