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Speed up bar's base aligners: pecan, minipoa and abPOA - #2026

Merged

glennhickey merged 6 commits into

Oct 4, 2026

Merged

Speed up bar's base aligners: pecan, minipoa and abPOA#2026
glennhickey merged 6 commits into
masterfrom
pecan-speedup

Commits on Sep 27, 2026
- Make pecan a practical base aligner for progressive bar
  
  glennhickey
  and
  claude
  committed
  5cac8f8
Commits on Sep 28, 2026
- Make minipoa as accurate as abpoa in bar, and several times faster
  
  glennhickey
  and
  claude
  committed
  c28e345
- Bump minipoa to keep its horizontal gap states as bits
  
  glennhickey
  and
  claude
  committed
  6d15d7c
- Take abPOA from the ComparativeGenomicsToolkit fork, with packed DP rows
  
  glennhickey
  and
  claude
  committed
  232b092
Commits on Oct 2, 2026
- Pin cPecan, abPOA and minipoa to their merged branches
  
  glennhickey
  and
  claude
  committed
  edd9142
- Merge master into pecan-speedup
  
  glennhickey
  and
  claude
  committed
  d429818