Issues

• Sprinzl: 4-nt variable loops labelled 44,46,47,48 instead of 44,45,46,48 (found comparing with GtRNAdb 3)

  rnabioco/clover#43 · Filter by author lkwhite opened on Oct 19, 2026

• Readers should validate pipeline output schemas and record provenance

  enhancement
  rnabioco/clover#42 · Filter by author jmbilodeaux opened on Oct 15, 2026
  

• Positions use different coordinate systems across readers (bcerror adapter-inclusive vs odds ratios tRNA-only)

  bug
  rnabioco/clover#41 · Filter by author jmbilodeaux opened on Oct 15, 2026
  

• Sprinzl position mapping: choose one method and validate on E. coli/T4, yeast and human

  enhancement
  rnabioco/clover#40 · Filter by author jmbilodeaux opened on Oct 15, 2026
  

• One canonical tRNA ID across readers, Sprinzl coordinates, MODOMICS and structure plotting

  bug
  rnabioco/clover#39 · Filter by author jmbilodeaux opened on Oct 15, 2026
  

• plot_identity_structure() passes outlines instead of mapped to plot_tRNA_structure()

  rnabioco/clover#32 · Filter by author jmbilodeaux opened on May 21, 2026
  1

• find_sprinzl_id() assumes nuc- prefix not present in bundled coords

  rnabioco/clover#31 · Filter by author jmbilodeaux opened on May 21, 2026

• naming conventions are jidnacked

  rnabioco/clover#27 · Filter by author jmbilodeaux opened on Apr 13, 2026

• Convert GitHub Actions CI to pixi

  rnabioco/clover#24 · Filter by author jayhesselberth opened on Feb 26, 2026

• Bundle human Sprinzl coordinates from tRNAs-in-space

  rnabioco/clover#23 · Filter by author jayhesselberth opened on Feb 23, 2026

• plot_tRNA_structure() silently draws overlapping circles for duplicate positions

  rnabioco/clover#22 · Filter by author jayhesselberth opened on Feb 23, 2026

• plot_tRNA_structure() should accept Sprinzl positions natively

  rnabioco/clover#20 · Filter by author jayhesselberth opened on Feb 23, 2026

• Add MODOMICS modification annotation support

  rnabioco/clover#11 · Filter by author jayhesselberth opened on Feb 17, 2026