Issues

• Add Cool-Seq-Tool Mapper Lucid Figures to RTD

  GenomicMedLab/cool-seq-tool#473 · Filter by author jarbesfeld opened on Jun 11, 2026

• Remove service_meta from schemas

  GenomicMedLab/cool-seq-tool#470 · Filter by author jsstevenson opened on May 16, 2026

• UtaDatabase.get_newest_assembly_ac should return str | None, not a list

  enhancement
  Feature

  GenomicMedLab/cool-seq-tool#469 · Filter by author jsstevenson opened on May 15, 2026

• UTA: Remove legacy DB URL support

  GenomicMedLab/cool-seq-tool#468 · Filter by author korikuzma opened on May 14, 2026

• UTA: Remove table construction from pool constructor function

  GenomicMedLab/cool-seq-tool#467 · Filter by author korikuzma opened on May 14, 2026

• Protein coordinates should not be returned for c. UTR coordinates

  bug
  GenomicMedLab/cool-seq-tool#466 · Filter by author theferrit32 opened on Apr 7, 2026
  3

• Write functions for forward and reverse transcription and translation between alleles

  enhancement
  GenomicMedLab/cool-seq-tool#459 · Filter by author jsstevenson opened on Mar 7, 2026
  

• grch38_to_mane_c_p should validate input arguments

  bugpriority:low
  GenomicMedLab/cool-seq-tool#457 · Filter by author korikuzma opened on Feb 25, 2026

• align_mapper.p_to_g does not support split codons across exon junctions (e.g. BRAF N581S)

  enhancement
  GenomicMedLab/cool-seq-tool#453 · Filter by author Hui-zju opened on Jan 27, 2026
  1

• Add docker compose

  enhancementpriority:low
  GenomicMedLab/cool-seq-tool#448 · Filter by author jarbesfeld opened on Dec 29, 2025

• Retry network requests on failure

  bug
  GenomicMedLab/cool-seq-tool#444 · Filter by author zealws opened on Nov 25, 2025

• UTA Query for transcript is non-deterministic

  bugpriority:medium
  Bug

  GenomicMedLab/cool-seq-tool#435 · Filter by author zealws opened on Oct 7, 2025
  6

• UTA database recreates schema on startup

  bugpriority:medium
  Bug

  GenomicMedLab/cool-seq-tool#430 · Filter by author zealws opened on Sep 15, 2025
  

• Liftover fails for GRCh37 variants where the strand differs from GRCh38

  bug
  GenomicMedLab/cool-seq-tool#421 · Filter by author jarbesfeld opened on Aug 15, 2025
  1

• Add information about Ensembl transcripts to docs

  documentationpriority:low
  GenomicMedLab/cool-seq-tool#342 · Filter by author korikuzma opened on Jul 31, 2024
  1

• Add coordinate type to usage docs

  documentationpriority:low
  GenomicMedLab/cool-seq-tool#341 · Filter by author korikuzma opened on Jul 31, 2024
  1

  

• Move pydantic models to their respective module

  priority:lowtechnical debt
  GenomicMedLab/cool-seq-tool#336 · Filter by author korikuzma opened on Jul 31, 2024
  1

• SeqRepoAccess should support SeqRepoRESTDataProxy

  enhancementpriority:mediumstale-exempt
  GenomicMedLab/cool-seq-tool#307 · Filter by author korikuzma opened on Jul 5, 2024
  4

• Allow initialization of writeable SeqRepo instance

  enhancementpriority:low
  GenomicMedLab/cool-seq-tool#282 · Filter by author jsstevenson opened on Apr 8, 2024
  4

• Resolve S608 errors

  priority:mediumtechnical debt
  GenomicMedLab/cool-seq-tool#269 · Filter by author korikuzma opened on Feb 13, 2024
  4

• Reduce the number of tests

  priority:lowstaletest
  GenomicMedLab/cool-seq-tool#255 · Filter by author korikuzma opened on Jan 10, 2024
  3

• Remove unused methods/functions

  priority:lowtechnical debt
  GenomicMedLab/cool-seq-tool#246 · Filter by author korikuzma opened on Dec 27, 2023
  3

  

• Better naming in UTA database module

  priority:lowtechnical debt
  GenomicMedLab/cool-seq-tool#245 · Filter by author korikuzma opened on Dec 27, 2023
  2

• Gene name inputs

  enhancementstale-exempttechnical debt
  GenomicMedLab/cool-seq-tool#232 · Filter by author jsstevenson opened on Dec 26, 2023
  2

• Validate exon offsets in transcript_to_genomic_coordinates()

  enhancementpriority:mediumstale-exempt
  GenomicMedLab/cool-seq-tool#184 · Filter by author jsstevenson opened on Aug 7, 2023
  5