griffithlab/civicpy

Issues

• civicpy cache truncated?

  #148 opened 3 months ago by zhanyinx
  9

• GKS support

  #154 opened 16 days ago by ahwagner
  0

• therapy names aren't unique per Evidence, and Disease property field sometimes is not there

  #153 opened 2 months ago by abidalikashi
  2

• Add molecular profile component operators

  #143 opened 8 months ago by jsstevenson
  1

• Travis cannot pull test pkl

  #104 opened 8 months ago by ahwagner
  1

• Update pypi release to use trusted publisher

  #145 opened 8 months ago by korikuzma
  0

• civic.load_cache() is broken

  #141 opened 2 years ago by mapo9
  2

• Handle stale remote caches

  #142 opened 2 years ago by susannasiebert
  0

• search_variants_by_coordinates() does not work (v2.0.0)

  #134 opened 2 years ago by mapo9
  2

• Have docker image creation depend on pypi release for GH Actions

  #132 opened 2 years ago by korikuzma
  0

• ValueError("Can't use wildcard when searching for non-GRCh37 coordinates") when annotating VCFs with `*` ALT allele

  #121 opened 3 years ago by mano2991
  5

• is there any useful examples of how to use it

  #119 opened 3 years ago by asmlgkj
  0

• update civicpy hard cache behavior

  #108 opened 4 years ago by ahwagner
  0

• synonymous CIViC variants with `=` in the name (e.g. `E55= (c.165G>A)`) cause VCF creation to fail

  #110 opened 4 years ago by susannasiebert
  0

• civicpy-specific endpoints on CIViC production

  #69 opened 4 years ago by ahwagner
  2

• accessing civicrecords from local cache

  #106 opened 4 years ago by vipints
  8

• activity caching and search

  #101 opened 4 years ago by ahwagner
  0

• speed up tests

  #93 opened 5 years ago by ahwagner
  1

• Add testing for example Jupyter notebooks

  #62 opened 5 years ago by susannasiebert
  1

• Allow users to mistakenly use '-' for empty ref/alt

  #78 opened 5 years ago by ahwagner
  0

• Deprecate the `get_all_x_ids` methods

  #90 opened 5 years ago by susannasiebert
  0

• Add more fields to the VCF annotation output

  #88 opened 5 years ago by susannasiebert
  0

• Consider support for all active versions of Python 3

  #56 opened 5 years ago by ahwagner
  0

• improve test coverage

  #20 opened 5 years ago by ahwagner
  0

• validate coordinates

  #15 opened 6 years ago by ahwagner
  0

• No remote queries option

  #74 opened 5 years ago by ahwagner
  1

• run erro

  #64 opened 5 years ago by fanyucai1
  8

• allow caching of all objects by time period

  #10 opened 5 years ago by ahwagner
  0

• add support for revisions and projections

  #50 opened 5 years ago by ahwagner
  1

• Get variant by name

  #25 opened 5 years ago by ahwagner
  0

• Update documentation

  #60 opened 5 years ago by ahwagner
  2

• refactor object retrieval from cache

  #48 opened 5 years ago by ahwagner
  0

• Mock tests for update behavior

  #67 opened 5 years ago by ahwagner
  0

• Refactor vcf exports using a maintained vcf library

  #42 opened 5 years ago by ahwagner
  0

• add revision retrieval method to CivicRecord

  #46 opened 5 years ago by ahwagner
  1

• promote Source to first-class entity

  #13 opened 6 years ago by ahwagner
  0

• add provenance information

  #65 opened 5 years ago by ahwagner
  2

• Create figure of code example

  #57 opened 5 years ago by ahwagner
  0

• update_cache and load_cache behavior

  #59 opened 5 years ago by ahwagner
  0

• Separate out requirements in setup.py

  #58 opened 5 years ago by ahwagner
  0

• VCFWriter improvements

  #53 opened 5 years ago by susannasiebert
  0

• add variant_group support

  #45 opened 5 years ago by ahwagner
  0

• implement intermediate search strategies

  #38 opened 5 years ago by ahwagner
  0

• adjust `get_all` routines to not return rejected elements by default

  #31 opened 5 years ago by ahwagner
  1

• Make cache timeout configurable by env variable

  #36 opened 5 years ago by ahwagner
  0

• make remote cache location configurable by env variable

  #33 opened 5 years ago by ahwagner
  1

• Remote load cache

  #17 opened 5 years ago by ahwagner
  0

• add coverage tracking

  #19 opened 6 years ago by ahwagner
  0

• add travisCI

  #18 opened 6 years ago by ahwagner
  0

• enable coordinate searching

  #12 opened 6 years ago by ahwagner
  1