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CHANGELOG.md

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CHANGELOG

v1.3.12 (August 2024)

  • Improvement: annotate_hits.py has a new argument to specify more GFF types to use
  • Improvement: count_patterns.py has a new argument to only print the p-value threshold (thanks to Bamu Damaris)
  • Bugfix: refuse to run if certain arguments are not provided
  • Docs: fix readthedocs' configuration
  • CI: speeding things up using mamba
  • CI: workaround to avoid GH actions crashing due to glmnet_py
  • Tests: avoid failures due to newer versions of sklearn

v1.3.11 (May 2023)

  • Improvement: Rtab files can use a empty string to signify missing values
  • Bugfix: avoid crashes wn running wgGWAS with covariates
  • Bugfix (summarise_annotations.py): more robust parsing
  • Bugfix: avoid crashes when distance matrices are not squared
  • Bugfix: properly format output when using --no-distances

v1.3.10 (July 2022)

  • Docs: more clarity on effect sizes for LMM
  • Bugfix (similarity): make sure the script actually uses all variants
  • Bugfix (QQ-plot): avoid axis inversion with newer versions of statsmodels (thanks to Julian Libiseller-Egger)
  • Bugfix: use kwargs when invoking functions from scikit-learn
  • Bugfix (annotate hits): avoid crashes when full path to reference genomes contains non-ASCII chars
  • Bugfix: WG models should not be ran with the --output-patterns function
  • Bugfix: avoid a crash when saving a WG model with covariates
  • Bugfix: add the "lineage" header when running a whole genome model

v1.3.9 (June 2021)

  • Bugfix: avoid a crash when providing lineages in whole genome mode

v1.3.8 (May 2021)

  • Improvement: fall back to Firth regression when encountering a matrix inversion error (thanks to Julian Libiseller-Egger)
  • Bugfix: check for zero passing variants in read_all (enet, thanks to Julian Libiseller-Egger)
  • Bugfix: use len(all_strains) instead of len(sample_order) to determine shape of sparse matrix in load_all_vars (enet, thanks to Julian Libiseller-Egger)
  • Bugfix: properly report all filtered variants
  • Bugfix: --lmm requires either --similarity or a LMM cache

v1.3.7 (May 2021)

  • Enhancement: check that provided phenotypes are of numeric type
  • Bugfix: properly report all filtered variants
  • Bugfix: don't crash if regression fails for missing data
  • Bugfix for whole genome regression and lineages
  • Bugfix/docs: properly report that the covariates file should have a header
  • scripts/summarise_annotations.py can work with unadjusted p-values (new option, thanks to Lindsay Clark)
  • scripts/phylogeny_distance.py: no need to reroot twice with updated dendropy
  • CI: transition to GitHub actions

v1.3.6 (May 2020)

  • Bugfix for missing variants in VCF files (now properly handled)
  • Bugfixes for k-mer mapping (lack of annotation, bwa fastmap with many hits
  • Explicitly look for duplicated samples in input files
  • Removed package from pypi (glmnet_py dependency could not be installed that way)

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