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joinReadsAndFilter: optional --allowDecoyOrphans orphan recovery C/C++ CI #341: Commit 1c78859 pushed by rob-p
22s codex/for-salmon
codex/for-salmon
22s
fix(chain): count decoy hits in fillMemCollection (decoy/transcript e… C/C++ CI #340: Commit 0fa5563 pushed by rob-p
27s codex/for-salmon
codex/for-salmon
27s
fix(sam): don't mutate qa.fragLen when clamping TLEN (salmon #1010) C/C++ CI #339: Commit 41a9245 pushed by rob-p
24s codex/for-salmon
codex/for-salmon
24s
feat(map): orphansRequireUnmappedMate orphan-emission policy C/C++ CI #338: Commit 8441f02 pushed by rob-p
24s codex/for-salmon
codex/for-salmon
24s
fix(map): inclusive fragment-length bound + orphan-rescue (salmon rus… C/C++ CI #337: Commit 17e1ccf pushed by rob-p
36s codex/for-salmon
codex/for-salmon
36s
Fix k-mer orientation in streaming getRefPos (non-canonical seed mis-… C/C++ CI #336: Commit 5dce7f4 pushed by rob-p
35s codex/for-salmon
codex/for-salmon
35s
Revert "PuffAligner: liberal flank-extension cutoff so good flanks ar… C/C++ CI #335: Commit c767f54 pushed by rob-p
36s codex/for-salmon
codex/for-salmon
36s
PuffAligner: liberal flank-extension cutoff so good flanks aren't dro… C/C++ CI #334: Commit f4dcec8 pushed by rob-p
41s codex/for-salmon
codex/for-salmon
41s
Use explicit atomic load/store in CandidateOccurence copy ops C/C++ CI #333: Commit ace68c1 pushed by rob-p
25s codex/for-salmon
codex/for-salmon
25s
Fix atomic copy-assignment in CandidateOccurence for Clang 19 C/C++ CI #332: Commit 07eb89c pushed by rob-p
27s codex/for-salmon
codex/for-salmon
27s
Validate k is odd, add optional minimizer length (-m) for SSHash C/C++ CI #331: Commit 4352415 pushed by rob-p
24s codex/for-salmon
codex/for-salmon
24s
Fix locale-aware number formatting in log messages C/C++ CI #330: Commit 81b6622 pushed by rob-p
25s codex/for-salmon
codex/for-salmon
25s
Update vendored libdivide to upstream 5.3.0 C/C++ CI #329: Commit 0efa7b6 pushed by rob-p
29s codex/for-salmon
codex/for-salmon
29s
Fix divider equality member access for clang builds C/C++ CI #328: Commit 1f0dd50 pushed by rob-p
35s codex/for-salmon
codex/for-salmon
35s
Use digestpp string absorb overloads to avoid GCC bounds warnings C/C++ CI #327: Commit 13fa733 pushed by rob-p
25s codex/for-salmon
codex/for-salmon
25s
Handle ReadSet<1>/KSeq/read-view variants in SAMWriter C/C++ CI #326: Commit 80072a8 pushed by rob-p
28s codex/for-salmon
codex/for-salmon
28s
Make SAMWriter compatible with pair-view and KSeq read types C/C++ CI #325: Commit 552fbd4 pushed by rob-p
27s codex/for-salmon
codex/for-salmon
27s
Refresh vendored async++ to upstream HEAD C/C++ CI #324: Commit 51c0f1d pushed by rob-p
36s codex/for-salmon
codex/for-salmon
36s
Update vendored FQFeeder/FastxParser to semi-working-generic-arity API C/C++ CI #323: Commit b4dd79d pushed by rob-p
28s codex/for-salmon
codex/for-salmon
28s
Modernize queue and iterator headers for GCC 13 warnings C/C++ CI #322: Commit 08399ea pushed by rob-p
26s codex/for-salmon
codex/for-salmon
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Fix compiler warnings: unused variable, unused typedef, deprecated st… C/C++ CI #321: Commit 77f0c0b pushed by rob-p
51s codex/for-salmon
codex/for-salmon
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Guard AVX2 ksw2 declaration and calls behind #ifndef KSW_USE_ARM C/C++ CI #320: Commit 0b6ded2 pushed by rob-p
37s codex/for-salmon
codex/for-salmon
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Optimize query/chaining/alignment hot paths (~22% wall-time improvement) C/C++ CI #319: Commit c846e90 pushed by rob-p
33s codex/for-salmon
codex/for-salmon
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Move SSHash template instantiation out of submodule C/C++ CI #318: Commit 8070da7 pushed by rob-p
26s codex/for-salmon
codex/for-salmon
26s
Fix fmt 12 format specifiers and clean up stale index files C/C++ CI #317: Commit 3477829 pushed by rob-p
33s codex/for-salmon
codex/for-salmon
33s