biocommons/hgvs

Issues

• Dataprovider - get canonical / MANE transcript

  #747 opened 5 months ago by davmlaw
  3

• Issue: Inconsistent normalization results compared to Mutalyzer

  #749 opened 2 months ago by chaopower-zhang
  5

• Context view improvements

  #741 opened 7 months ago by andreasprlic
  3

• hgvs_c to hgvs_p projection throws IndexError for "NM_001253909.2:c.416_417insGTG"

  #707 opened 4 months ago by holtgrewe
  2

• Is it possible to get hgvs official name from "15-49716528-A-G"？

  #743 opened 5 months ago by shizipo
  2

• Normalizer constructor doesn't pass the `validate` param to the VariantMapper constructor

  #704 opened 5 months ago by mihaitodor
  5

• Support transcript identifiers (in parentheses) in variants

  #735 opened 9 months ago by marius-mather
  1

• babelfish VCF to g.HGVS fails when contig accession used as chromosome name

  #744 opened 6 months ago by davmlaw
  0

• c_to_p at intron/exon boundary where splice region is preserved

  #714 opened a year ago by b0d0nne11
  3

• c_to_p for dups that start in transcript but end in UTR

  #715 opened 7 months ago by b0d0nne11
  10

• Global configuration item not always being used

  #736 opened 8 months ago by wlymanambry
  0

• Modify parser to include common errors to provide better error messages than "syntax error"

  #720 opened a year ago by davmlaw
  3

• Make data provider config explicit

  #645 opened a year ago by reece
  5

• Use kitchensinksetup in all tests

  #644 opened 7 months ago by reece
  5

• Support for circular genomic identifiers

  #650 opened a year ago by mbiokyle29
  4

• mitochondria (m.) assembly mapping

  #663 opened a year ago by davmlaw
  7

• Support transcript variants with specification of underlying genomic reference

  #642 opened a year ago by reece
  4

• How to properly handle selenoproteins

  #710 opened a year ago by holtgrewe
  3

• Investigate and improve hgvs performance

  #721 opened 7 months ago by reece
  2

• p type cannot be validated

  #727 opened a year ago by markgene
  1

• Update default config to uta v20210129b?

  #733 opened 8 months ago by larrybabb
  0

• Consider exposing a utility for converting between g. variants by leveraging pyliftover

  #711 opened 10 months ago by mihaitodor
  6

• Babelfish vcf conversion errors - case sensitivity, multi-base identities

  #722 opened 9 months ago by davmlaw
  1

• CDS phase (frame offset for eg ribo slippage) not taken into account in amino acid translation

  #732 opened 9 months ago by davmlaw
  0

• Exon boundary / intron validation - need for genome build specific validation?

  #700 opened a year ago by davmlaw
  4

• Inconsistencies across intron/exon boundaries

  #655 opened 2 years ago by cassiemk
  6

• Validation - refactor to be able to retrieve all errors rather than throw exception on 1st

  #706 opened a year ago by davmlaw
  5

• Update / modernize packaging

  #691 opened a year ago by reece
  4

• For start loss AARefAlt.format always returns 3 letter amino acid even when single letter amino acid is configured

  #730 opened 9 months ago by jPleyte
  0

• `Normalizer.normalize()` is performing sequence position validation which cannot be skipped

  #705 opened a year ago by mihaitodor
  4

• Remove top level code environment scripts from modules

  #695 opened a year ago by ecalifornica
  3

• Remove __future__ module usage

  #688 opened a year ago by ecalifornica
  0

• `g_to_t` for promoter regions

  #724 opened a year ago by markgene
  2

• Problems hgvs between build 37 and 38

  #718 opened a year ago by jeantristanb
  4

• setup.cfg metadata

  #701 opened a year ago by davmlaw
  2

• Coordinate is out of bounds error when roundtripping GRCh38 variants via `g_to_c` + `c_to_g` and `relevant_transcripts`

  #717 opened a year ago by mihaitodor
  5

• make develop not working

  #712 opened a year ago by andreasprlic
  1

• Liftover hgvs nomenclature from hg19 to hg38

  #703 opened a year ago by vlakhujani
  1

• Do I need to develop specific transcript？

  #649 opened a year ago by user-tq
  5

• update readme/documentation for local installation

  #692 opened a year ago by katiestahl
  0

• c_to_p predicts "p.?" rather than "p.Met1?" for "NM_206926.1:c.1A>G"

  #651 opened a year ago by holtgrewe
  7

• HGVSParseError for gene symbols with "-" (dashes) in them

  #670 opened a year ago by davmlaw
  4

• Cannot import Parser due to circular import

  #689 opened a year ago by davmlaw
  1

• Improve Parser startup time by storing generated Python code

  #661 opened a year ago by davmlaw
  2

• Error: AttributeError: 'UTA_postgresql' object has no attribute '_pool'

  #652 opened a year ago by hotsoupisgood
  2

• Babelfish - support VCF symbolic alts eg <DEL> and <DUP>

  #665 opened a year ago by davmlaw
  1

• Does this library have support for "?" as HGVS does?

  #682 opened a year ago by wlymanambry
  1

• Equivalent genomic coordinates for transcript structure

  #667 opened a year ago by wlymanambry
  2

• Is it possible to get exon information and/or gene name for a given transcript?

  #658 opened a year ago by wlymanambry
  5

• Babelfish.hgvs_to_vcf tests against length_change signature not method result

  #653 opened 2 years ago by davmlaw
  1