Issues

• 5-Base: --illumina_5base --bowtie2: "failed to write BAM record: I/O error: read length-sequence length mismatch" partway through alignment, in both --local and end-to-end modes

  FelixKrueger/Bismark#1125 · Filter by author ryancey1 opened on Sep 30, 2026

• feat(aligner): FIFO streaming for the converted temp reads (disk-constrained runs)

  FelixKrueger/Bismark#1120 · Filter by author ewels opened on Sep 11, 2026
  1

• 5-Base: emit simplex (single-strand) consensus molecules alongside duplex

  FelixKrueger/Bismark#1104 · Filter by author FelixKrueger opened on Aug 14, 2026

• 5-Base: validate --five_base_index at resolve time instead of failing late as a desync

  FelixKrueger/Bismark#1100 · Filter by author FelixKrueger opened on Aug 10, 2026

• 5-Base: --illumina_5base wrongly requires the converted CT/GA indexes it never opens

  FelixKrueger/Bismark#1099 · Filter by author FelixKrueger opened on Aug 10, 2026

• 5-Base → wgbs_tools/UXM interop: re-encode XM into bisulfite-convention SEQ

  FelixKrueger/Bismark#1095 · Filter by author FelixKrueger opened on Aug 5, 2026
  10

• Bismark (Perl) is in maintenance freeze — new work targets the Rust suite

  FelixKrueger/Bismark#1010 · Filter by author FelixKrueger opened on Jun 22, 2026