Issues

• Mapping fails with a 500 when the mapper's UTA connection times out during transcript selection

  app: mapper
  Bug

  VariantEffect/dcd_mapping2#123 · Filter by author bencap opened on Nov 2, 2026

• BLAT killed for running out of memory is reported as an alignment failure, so mapping is never retried

  app: mapper
  Bug

  VariantEffect/dcd_mapping2#122 · Filter by author bencap opened on Oct 23, 2026 · R2026.4

• Importing dcd_mapping fails when NCBI's FTP server is unreachable

  app: mapper
  Bug

  VariantEffect/dcd_mapping2#119 · Filter by author bencap opened on Oct 20, 2026

• Choose the BLAT hit that aligns the most of the target, not the one nearest the gene start

  app: mapper
  Bug

  VariantEffect/dcd_mapping2#112 · Filter by author bencap opened on Oct 11, 2026 · R2026.4

• Remove underscore from check for Ensembl Protein ID

  VariantEffect/dcd_mapping2#109 · Filter by author davereinhart opened on Jul 7, 2026

• Incorrect mapping of CHEK2

  app: worker
  Bug

  VariantEffect/dcd_mapping2#107 · Filter by author jstone-dev opened on Jun 14, 2026

• Migrate dcd_mapping from VRS Haplotype to CisPhasedBlock (requires dependency-stack modernization)

  app: mapper
  Task

  VariantEffect/dcd_mapping2#104 · Filter by author bencap opened on Jun 4, 2026

• feat: Cross-level translation for multivariant assay inputs (haplotypes + multi-AA delins)

  app: mapper
  Feature

  VariantEffect/dcd_mapping2#103 · Filter by author bencap opened on Jun 2, 2026
  

• refactor: Unify duplicated CLI and API mapping execution flows

  VariantEffect/dcd_mapping2#102 · Filter by author bencap opened on Jun 1, 2026

• Mark intronic variants with a dedicated consequence instead of raising a mapping error

  app: backendapp: mapper
  Feature

  VariantEffect/dcd_mapping2#99 · Filter by author bencap opened on May 6, 2026

• Decide on preferred form (and/or formalize current handling) for reference-identical HGVS variants

  app: mapperneeds: discussion
  Feature

  VariantEffect/dcd_mapping2#93 · Filter by author bencap opened on Apr 15, 2026

• Define response protocols for mapping flags

  app: mapperneeds: discussion
  Spike

  VariantEffect/dcd_mapping2#92 · Filter by author bencap opened on Apr 10, 2026
  1

• Surface alignment visualization on suspect mappings

  app: backendapp: databaseapp: mapper
  Feature

  VariantEffect/dcd_mapping2#91 · Filter by author bencap opened on Apr 10, 2026

• Flag alignment ambiguity when top candidates are close in score

  app: backendapp: databaseapp: mapper
  Feature

  VariantEffect/dcd_mapping2#90 · Filter by author bencap opened on Apr 10, 2026

• Extract and store reference sequence discrepancies from alignment output

  app: backendapp: databaseapp: mapper
  Feature

  VariantEffect/dcd_mapping2#89 · Filter by author bencap opened on Apr 10, 2026

• Implement a mapped variant status taxonomy

  app: backendapp: databaseapp: mapper
  Feature

  VariantEffect/dcd_mapping2#88 · Filter by author bencap opened on Apr 10, 2026 · R2026.4

• Make the mapper more opinionated about alignment uncertainty

  app: backendapp: databaseapp: frontendapp: mapper
  Feature

  VariantEffect/dcd_mapping2#85 · Filter by author bencap opened on Apr 10, 2026

• Variant representation in HGVS and VRS for multi-base variants that affect a single codon

  app: mapperneeds: discussion
  Spike

  VariantEffect/dcd_mapping2#84 · Filter by author sallybg opened on Apr 8, 2026
  1

• Look into whether intronic variants are already supported by GA4GH VRS library and/or Biocommons HGVS library.

  app: backendapp: mapper
  Spike

  VariantEffect/dcd_mapping2#83 · Filter by author sallybg opened on Apr 8, 2026
  1

  

• Include cdna transcript information in post-mapped metadata for accession-based score sets

  app: mapper
  VariantEffect/dcd_mapping2#81 · Filter by author sallybg opened on Mar 12, 2026

• Integrate upstream commits

  app: mapper
  Task

  VariantEffect/dcd_mapping2#77 · Filter by author bencap opened on Feb 24, 2026

• Bump cool-seq-tool + gene_normalizer

  app: mapper
  Task

  VariantEffect/dcd_mapping2#60 · Filter by author bencap opened on Nov 13, 2025

• Place a target from its declared accession and offset when its sequence confirms them

  app: mapper
  Feature

  VariantEffect/dcd_mapping2#58 · Filter by author bencap opened on Aug 11, 2025

• Flag for BLAT Caching in Development

  app: mapper
  Feature

  VariantEffect/dcd_mapping2#54 · Filter by author bencap opened on Jul 29, 2025

• Cross-validate Mapper Generated HGVS Strings w/ Pillar Project Mappings

  app: mapper
  Task

  VariantEffect/dcd_mapping2#49 · Filter by author bencap opened on Jun 25, 2025