biocommons/hgvs

Issues

• Issue: Inconsistent normalization results compared to Mutalyzer

  #749 opened 3 months ago
  5

• Dataprovider - get canonical / MANE transcript

  #747 opened 5 months ago
  3

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

  #744 opened 7 months ago
  0

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

  #743 opened 5 months ago
  2

• Context view improvements

  #741 opened 7 months ago
  4

• Global configuration item not always being used

  #736 opened 9 months ago
  1

• Support transcript identifiers (in parentheses) in variants

  #735 opened 9 months ago
  1

• Update default config to uta v20210129b?

  #733 opened 9 months ago
  0

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

  #732 opened 10 months ago
  0

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

  #730 opened 10 months ago
  0

• p type cannot be validated

  #727 opened a year ago
  1

• `g_to_t` for promoter regions

  #724 opened a year ago
  2

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

  #722 opened 10 months ago
  1

• Investigate and improve hgvs performance

  #721 opened 8 months ago
  2

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

  #720 opened a year ago
  3

• Problems hgvs between build 37 and 38

  #718 opened a year ago
  4

• 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
  5

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

  #715 opened 7 months ago
  10

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

  #714 opened a year ago
  3

• make develop not working

  #712 opened a year ago
  1

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

  #711 opened a year ago
  6

• How to properly handle selenoproteins

  #710 opened a year ago
  3

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

  #707 opened 4 months ago
  2

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

  #706 opened a year ago
  5

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

  #705 opened a year ago
  4

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

  #704 opened 5 months ago
  5

• Liftover hgvs nomenclature from hg19 to hg38

  #703 opened a year ago
  1

• setup.cfg metadata

  #701 opened a year ago
  2

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

  #700 opened a year ago
  4

• Remove top level code environment scripts from modules

  #695 opened a year ago
  3

• update readme/documentation for local installation

  #692 opened a year ago
  0

• Update / modernize packaging

  #691 opened a year ago
  4

• Cannot import Parser due to circular import

  #689 opened a year ago
  1

• Remove __future__ module usage

  #688 opened a year ago
  0

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

  #682 opened a year ago
  1

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

  #670 opened a year ago
  4

• Equivalent genomic coordinates for transcript structure

  #667 opened a year ago
  2

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

  #665 opened a year ago
  1

• mitochondria (m.) assembly mapping

  #663 opened 2 years ago
  7

• Improve Parser startup time by storing generated Python code

  #661 opened a year ago
  2

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

  #658 opened a year ago
  5

• Inconsistencies across intron/exon boundaries

  #655 opened 2 years ago
  6

• Babelfish.hgvs_to_vcf tests against length_change signature not method result

  #653 opened 2 years ago
  1

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

  #652 opened a year ago
  2

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

  #651 opened a year ago
  7

• Support for circular genomic identifiers

  #650 opened 2 years ago
  4

• Do I need to develop specific transcript？

  #649 opened a year ago
  5

• Make data provider config explicit

  #645 opened 2 years ago
  5

• Use kitchensinksetup in all tests

  #644 opened 8 months ago
  5

• Support transcript variants with specification of underlying genomic reference

  #642 opened 2 years ago
  4