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CHANGELOG

v1.3.5 (March 2020)

  • Bugfix for covariates samples mismatching for LMM
  • Bugfix for numeric sample names
  • Bugfix for crashes happening during enet variants filtering
  • Fix pip and setup.py installs (glmnet_py)
  • Remove deprecation warnings for fastlmm

v1.3.4 (December 2019)

  • Update installation from pip and setup.py
  • Allow multiple intervals for a single burden tests

v1.3.3 (September 2019)

  • Fix for multiple reported alignments from bwa

v1.3.2 (September 2019)

  • Features, bugfixes and documentation for prediction
  • Bugfix for multiple hits/overlapping regions in annotate hits

v1.3.1 (July 2019)

  • Handle API changes between different statsmodels versions
  • Handle corner cases where no distance matrix is provided but --no-distances should be used

v1.3.0 (June 2019)

  • Handle missing variants as missing (with new --max-missing option to control maximum allowed)
  • Unit testing for enet functionality
  • Added option to perform midpoint rooting on tree used by phylogeny_distance.py
  • Updated docs with a new section about the use of unitigs
  • Various bugfixes
    • Checks on phenotypes file
    • Improved BWA command and results handling
    • New optimizer for fit_null
    • Avoid deprecation warnings from pandas
    • Report to user if multiple chromosome/contigs are found while mapping
    • Use the correct samples order when using lineages and covariates

v1.2.0 (November 2018)

  • Added elastic net functionality
  • Avoid exiting with error in python 3.7+
  • Allow spaces in Rtab's COG names
  • Make unit tests compatible with python 2

v1.1.2 (October 2018)

  • Bugfix for sample names interpreted as integers
  • Bugfix for user-defined lineages
  • Small fixes in docs and README

v1.1.1 (June 2018)

  • Further bugfixes for the annotation of kmers
  • Platform specific pandas bugfix with LMM
  • Test kmers annotation
  • Improved README

v1.1.0 (May 2018)

  • New option (--no-distances) to run fixed effects associations without a distance matrix
  • New option (--print-filtered) allowing to print variants not passing filters
  • Check for consistency between lmm and lineage samples
  • Add lineage to phandango mapping output
  • annotate_hits_pyseer: properly parse GFF3 entries
  • annotate_hits_pyseer: map all possible kemrs for reference genomes
  • Update docs
  • Tests are less dependent on machine precision

v1.0.2 (Mar 2018)

  • Better dependencies definition

v1.0.1 (Mar 2018)

  • Check for missing values in VCF entries

v1.0.0 (Feb 2018)

  • First release