v1.0.0

Highlights

New features and API changes

• Ag3: Added support for genome regions when accessing data
  (GH14). N.B.,
  the contig parameter is no longer supported, instead use the
  region parameter which can be a contig ID (e.g., "3L"), a contig
  region (e.g., "3L:1000000-2000000"), a gene ID ("AGAP004070"), or a
  list of any of the above. This affects methods including
  snp_sites(), site_filters(), snp_genotypes() and
  snp_dataset(). Contributed by Nace
  Kranjc.

• Ag3: The parameters for specifying which species analysis version
  is used have changed
  (GH55). This
  affects species_calls(), sample_metadata(),
  snp_allele_frequencies() and gene_cnv_frequencies(). In most
  cases the default values for these parameters should be appropriate
  and so no changes to your code should be needed.

• Ag3: The names of the columns in dataframes containing data
  related to species calling have changed to make it clearer which
  species calling method has been used. This affects dataframes
  returned by species_calls() and sample_metadata(). See
  GH93
  for further details.

• Ag3: The latest cohorts metadata are now automatically loaded and
  joined in with the sample metadata when calling
  sample_metadata(). See
  GH94
  for further details.

• Ag3: SNP effects are now automatically included in the output
  dataframe from snp_allele_frequencies()
  (GH95).

• Ag3: Added a new sample_query parameter to methods returning
  frequencies to allow for making a sub-selection of samples
  (GH96).

• Ag3: Added a new method aa_allele_frequencies() to return a
  dataframe of amino acid substitution allele frequencies
  (GH101).

• Ag3: Added a new method plot_frequencies_heatmap() for creating
  a heatmap plot of allele frequencies
  (GH102).

• Ag3: The Google Cloud Storage URL ("gs://vo_agam_release") is now
  the default value when instantiating the Ag3 class
  (GH103). So
  now you don't need to provide it if you are accessing data from
  GCS. I.e., you can just do:

import malariagen_data
ag3 = malariagen_data.Ag3()

• Ag3: The identifiers used for data releases have been changed to
  use "3.0" instead of "v3", "3.1" instead of "v3.1",
  etc. (GH104)

• The Ag3 and Amin1 classes have a better repr
  (GH111).

• Ag3: All dataframe columns containing allele frequency values are
  now prefixed with "frq_" to allow for easier selection of frequency
  columns
  (GH116).

• Ag3: When computing frequencies, automatically drop columns for
  cohorts below the minimum cohort size
  (GH118).

• Amin1: Added support for region parameter instead of contig
  (GH119).

• Ag3: The snp_sites() method no longer returns a tuple of arrays
  if the field parameter is not provided, please provide an explicit
  field parameter or use the snp_calls() method instead
  (recommended).

Bug fixes, maintenance and documentation

• Ag3: Move default values for analysis parameters to constants
  (GH70).

• Ag3: Check for manifest.tsv when discovering a release
  (GH74).

• Ag3: Decode sample IDs when building snp_calls() dataset
  (GH82).

• Ag3: Fix snp_calls() cannot take multiple releases for
  sample_set parameter
  (GH85).

• Ag3: Fix chunks parameter appears to be ignored
  (GH86).

• Support Python 3.9
  (GH91).

• Ag3: Fix pandas performance warnings
  (GH108).

• Ag3: Fix bug involving inconsistent array lengths before and after
  computation
  (GH114).

• Ag3: Fix compatibility with zarr 2.11.0
  (GH129).

• Some optimisations to speed up the test suite a bit
  (GH122).

Pull requests

• Add variance vars to CNV HMM by @leehart in #83
• Support multiple releases via the sample_sets parameter by @alimanfoo in #88
• Upgrade CI by @alimanfoo in #92
• Improve species metadata by @alimanfoo in #97
• Check release manifest by @alimanfoo in #98
• Decode sample_id to str in Ag3.snp_calls() dataset by @alimanfoo in #99
• Add effects to allele frequencies by @alimanfoo in #100
• Support genomic regions by @nkran in #106
• snp_allele_frequencies() Pandas Warning - fragmented dataframe by @cclarkson in #110
• Add cohorts to sample_metadata() by @cclarkson in #109
• Misc minor improvements by @alimanfoo in #112
• Add "frq_" to columns in frequency generating methods by @cclarkson in #117
• Drop cohorts columns below min cohort size when computing frequencies by @cclarkson in #120
• Fix bug with optimised dask compress by @alimanfoo in #121
• ag3.aa_allele_frequencies() method by @cclarkson in #124
• Add sample_query parameter to allele frequencies by @alimanfoo in #126
• ag3.plot_frequencies_heatmap() by @cclarkson in #125
• Zarr 2.11.0 compatibility by @alimanfoo in #130
• v1.0.0 release notes by @alimanfoo in #131
• Refactor region support and add region support to Amin1 by @alimanfoo in #132

New Contributors

• @leehart made their first contribution in #83
• @nkran made their first contribution in #106

Full Changelog: v0.15.0...v1.0.0