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Correct pileup record state and count accounting - #656

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SuhasSrinivasan wants to merge 8 commits into

nanoporetech:masterfrom

SuhasSrinivasan:codex/normalize-duplicate-pileup-modified-bases

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Correct pileup record state and count accounting#656
SuhasSrinivasan wants to merge 8 commits into
nanoporetech:masterfrom
SuhasSrinivasan:codex/normalize-duplicate-pileup-modified-bases

Commits on Aug 5, 2026
- Count all combined cytosine calls
  SuhasSrinivasan
  committed
  ae25fa7
- Allow overlapping optimized motif masks
  SuhasSrinivasan
  committed
  9f321e1
- Fix compact dynamic combine slots
  SuhasSrinivasan
  committed
  e9646c9
- Key dynamic modification slots by base and code
  SuhasSrinivasan
  committed
  7c20fb5
- Harden dynamic pileup slot tests
  SuhasSrinivasan
  committed
  9b5e93c
- Align dynamic reverse pileup status counts
  SuhasSrinivasan
  committed
  2ca7b1f
- Normalize duplicate pileup modification selections
  SuhasSrinivasan
  committed
  b060d18
Commits on Aug 11, 2026
- Clear generic pileup state between records
  SuhasSrinivasan
  committed
  18b3ff2