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• joinReadsAndFilter: optional --allowDecoyOrphans orphan recovery

  failed:
  C/C++ CI#341:Commit1c78859pushedbyrob-p
  codex/for-salmon

  Jun 19, 202622s
  More actions for workflow run 341

• fix(chain): count decoy hits in fillMemCollection (decoy/transcript e…

  failed:
  C/C++ CI#340:Commit0fa5563pushedbyrob-p
  codex/for-salmon

  Jun 19, 202627s
  More actions for workflow run 340

• fix(sam): don't mutate qa.fragLen when clamping TLEN (salmon #1010)

  failed:
  C/C++ CI#339:Commit41a9245pushedbyrob-p
  codex/for-salmon

  Jun 19, 202624s
  More actions for workflow run 339

• feat(map): orphansRequireUnmappedMate orphan-emission policy

  failed:
  C/C++ CI#338:Commit8441f02pushedbyrob-p
  codex/for-salmon

  Jun 19, 202624s
  More actions for workflow run 338

• fix(map): inclusive fragment-length bound + orphan-rescue (salmon rus…

  failed:
  C/C++ CI#337:Commit17e1ccfpushedbyrob-p
  codex/for-salmon

  Jun 18, 202636s
  More actions for workflow run 337

• Fix k-mer orientation in streaming getRefPos (non-canonical seed mis-…

  failed:
  C/C++ CI#336:Commit5dce7f4pushedbyrob-p
  codex/for-salmon

  Jun 10, 202635s
  More actions for workflow run 336

• Revert "PuffAligner: liberal flank-extension cutoff so good flanks ar…

  failed:
  C/C++ CI#335:Commitc767f54pushedbyrob-p
  codex/for-salmon

  Jun 10, 202636s
  More actions for workflow run 335

• PuffAligner: liberal flank-extension cutoff so good flanks aren't dro…

  failed:
  C/C++ CI#334:Commitf4dcec8pushedbyrob-p
  codex/for-salmon

  Jun 10, 202641s
  More actions for workflow run 334

• Use explicit atomic load/store in CandidateOccurence copy ops

  failed:
  C/C++ CI#333:Commitace68c1pushedbyrob-p
  codex/for-salmon

  Mar 11, 202625s
  More actions for workflow run 333

• Fix atomic copy-assignment in CandidateOccurence for Clang 19

  failed:
  C/C++ CI#332:Commit07eb89cpushedbyrob-p
  codex/for-salmon

  Mar 11, 202627s
  More actions for workflow run 332

• Validate k is odd, add optional minimizer length (-m) for SSHash

  failed:
  C/C++ CI#331:Commit4352415pushedbyrob-p
  codex/for-salmon

  Mar 11, 202624s
  More actions for workflow run 331

• Fix locale-aware number formatting in log messages

  failed:
  C/C++ CI#330:Commit81b6622pushedbyrob-p
  codex/for-salmon

  Mar 11, 202625s
  More actions for workflow run 330

• Update vendored libdivide to upstream 5.3.0

  failed:
  C/C++ CI#329:Commit0efa7b6pushedbyrob-p
  codex/for-salmon

  Mar 10, 202629s
  More actions for workflow run 329

• Fix divider equality member access for clang builds

  failed:
  C/C++ CI#328:Commit1f0dd50pushedbyrob-p
  codex/for-salmon

  Mar 10, 202635s
  More actions for workflow run 328

• Use digestpp string absorb overloads to avoid GCC bounds warnings

  failed:
  C/C++ CI#327:Commit13fa733pushedbyrob-p
  codex/for-salmon

  Mar 10, 202625s
  More actions for workflow run 327

• Handle ReadSet<1>/KSeq/read-view variants in SAMWriter

  failed:
  C/C++ CI#326:Commit80072a8pushedbyrob-p
  codex/for-salmon

  Mar 10, 202628s
  More actions for workflow run 326

• Make SAMWriter compatible with pair-view and KSeq read types

  failed:
  C/C++ CI#325:Commit552fbd4pushedbyrob-p
  codex/for-salmon

  Mar 10, 202627s
  More actions for workflow run 325

• Refresh vendored async++ to upstream HEAD

  failed:
  C/C++ CI#324:Commit51c0f1dpushedbyrob-p
  codex/for-salmon

  Mar 10, 202636s
  More actions for workflow run 324

• Update vendored FQFeeder/FastxParser to semi-working-generic-arity API

  failed:
  C/C++ CI#323:Commitb4dd79dpushedbyrob-p
  codex/for-salmon

  Mar 10, 202628s
  More actions for workflow run 323

• Modernize queue and iterator headers for GCC 13 warnings

  failed:
  C/C++ CI#322:Commit08399eapushedbyrob-p
  codex/for-salmon

  Mar 10, 202626s
  More actions for workflow run 322

• Fix compiler warnings: unused variable, unused typedef, deprecated st…

  failed:
  C/C++ CI#321:Commit77f0c0bpushedbyrob-p
  codex/for-salmon

  Mar 10, 202651s
  More actions for workflow run 321

• Guard AVX2 ksw2 declaration and calls behind #ifndef KSW_USE_ARM

  failed:
  C/C++ CI#320:Commit0b6ded2pushedbyrob-p
  codex/for-salmon

  Mar 10, 202637s
  More actions for workflow run 320

• Optimize query/chaining/alignment hot paths (~22% wall-time improvement)

  failed:
  C/C++ CI#319:Commitc846e90pushedbyrob-p
  codex/for-salmon

  Mar 10, 202633s
  More actions for workflow run 319

• Move SSHash template instantiation out of submodule

  failed:
  C/C++ CI#318:Commit8070da7pushedbyrob-p
  codex/for-salmon

  Mar 10, 202626s
  More actions for workflow run 318

• Fix fmt 12 format specifiers and clean up stale index files

  failed:
  C/C++ CI#317:Commit3477829pushedbyrob-p
  codex/for-salmon

  Mar 10, 202633s
  More actions for workflow run 317