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4e77c94
feat: Improve very large comparison handling (prevent oom)
St4NNi Feb 20, 2026
71982fc
chore: Update dependencies
St4NNi Feb 20, 2026
afaeb48
feat: Update Bias feature to take an effective fscale
St4NNi Feb 20, 2026
1bdc45f
feat: Optimize LUT to use a better water filling / smoothing algorithm
St4NNi Feb 23, 2026
a7e72c3
feat: Added containment calculation correction and e-value
St4NNi Feb 25, 2026
40f3dd4
feat: Update validation functions
St4NNi Feb 25, 2026
58e81cc
feat: Added k21 comprehensive benchmark
St4NNi Mar 3, 2026
915ee98
fix: Fixed crash if c = 0.0
St4NNi Mar 4, 2026
9d3feee
feat: Better bias table benchmarks
St4NNi Mar 9, 2026
eeec51b
feat: Bias testing / optimizations
St4NNi Mar 11, 2026
dce8660
feat: Added simplified knapsack optimizer
St4NNi Mar 11, 2026
bfb68b8
fix: weighted sum calculation
St4NNi Mar 12, 2026
a263fc0
chore: Update README and actions
St4NNi Apr 28, 2026
fa57793
fix: Added stronger CMS validation
St4NNi Apr 28, 2026
b2fdc5f
fix: Prevent jamreader from missing earlier samples
St4NNi Apr 28, 2026
2d7978f
chore: try to reduce memory consumption and improve fastq splitting
St4NNi Apr 28, 2026
2837bfc
fix: query metrics and cutoff-filtering
St4NNi Apr 28, 2026
e6d0357
feat: Update query interpolation to be smarter in bias aware mode
St4NNi Apr 28, 2026
a64c42a
chore: Clippy and fmt fixes
St4NNi Apr 28, 2026
fb8ce4f
fix: reject incompatible JAM query sketches
St4NNi May 7, 2026
6ec4c52
chore: Dedup query hashes
St4NNi May 7, 2026
0ea318f
feat: check query sample ID overflow
St4NNi May 7, 2026
2508581
fix: Harden writer size checks to prevent overflows
St4NNi May 7, 2026
d5abc7e
chore: Harden jam reader validation
St4NNi May 7, 2026
472735f
feat: make bias drop mode reject all hashes
St4NNi May 7, 2026
0de9f8b
chore: remove bias LUT debug output
St4NNi May 7, 2026
160b31f
feat: Add force to dist output
St4NNi May 7, 2026
b1bae03
fix: Resolve file list paths relative to lists
St4NNi May 7, 2026
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6 changes: 4 additions & 2 deletions .github/workflows/push.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: dtolnay/rust-toolchain@nightly
- run: cargo test
- uses: dtolnay/rust-toolchain@stable
- run: cargo fmt --all -- --check
- run: cargo test --all-targets
- run: cargo clippy --all-targets --all-features -- -D warnings
11 changes: 10 additions & 1 deletion .github/workflows/release.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,16 @@ jobs:
uses: actions/checkout@v3
with:
submodules: recursive
- uses: dtolnay/rust-toolchain@stable
- name: Check formatting
run: cargo fmt --all -- --check
- name: Run tests
run: cargo test --all-targets
- name: Run clippy
run: cargo clippy --all-targets --all-features -- -D warnings
- name: Dry-run publish
run: cargo publish --dry-run
- name: Cargo publish
run: cargo publish --token ${CRATES_TOKEN}
env:
CRATES_TOKEN: ${{ secrets.CRATES_TOKEN }}
CRATES_TOKEN: ${{ secrets.CRATES_TOKEN }}
5 changes: 4 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -9,4 +9,7 @@
/testout
/tools/out
/tools/target
/tools/Cargo.lock
/tools/Cargo.lock
tests/testfiles/all*
tests/testfiles/plas*
tests/testfiles/chrom*
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