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Madhava/libs - #68

Merged

madhavajay merged 220 commits into

mainfrom

madhava/libs

Jun 4, 2026

Merged

Madhava/libs#68
madhavajay merged 220 commits into
mainfrom
madhava/libs

Commits on May 27, 2026
- Add BioScript library shim infrastructure
  madhavajay
  committed
  7e1aa18
- Add VNtyper BioScript port scaffolding
  madhavajay
  committed
  322870a
- Add bcftools wrapper surface
  madhavajay
  committed
  05ca7ce
- Gate VNtyper integration data tests
  madhavajay
  committed
  8e19017
- Split runtime tool method bindings
  madhavajay
  committed
  001122e
- Document VNtyper upstream inventory
  madhavajay
  committed
  35bb010
- Add VNtyper region helpers
  madhavajay
  committed
  0e7111f
- Add VNtyper command planner
  madhavajay
  committed
  b2623fc
- Mark VNtyper port skeleton milestone
  madhavajay
  committed
  7bad876
- Add optional VNtyper upstream scoring parity test
  madhavajay
  committed
  6a195cf
- Record VNtyper port decisions
  madhavajay
  committed
  cdc4bd6
- Add VNtyper expected fixture outputs
  madhavajay
  committed
  d16d70c
- Expand VNtyper structured report JSON
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  5ae3165
- Add VNtyper adVNTR report fields
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  c820af5
- Add initial VNtyper HTML report
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  committed
  678140b
- Record tool command planning timings
  madhavajay
  committed
  3925ef4
- Triage VNtyper optional modules
  madhavajay
  committed
  5fe525f
- Document Kestrel native port spike
  madhavajay
  committed
  2c3e441
- Gate VNtyper full pipeline prerequisites
  madhavajay
  committed
  152a932
- Add interactive VNtyper report controls
  madhavajay
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  6b7ec02
- Gate upstream VNtyper reference tests
  madhavajay
  committed
  d43990d
- Add VNtyper IGV report session
  madhavajay
  committed
  24dd37e
- Port VNtyper scoring unit cases
  madhavajay
  committed
  677bed0
- Port VNtyper flagging unit cases
  madhavajay
  committed
  984b562
- Port VNtyper motif filtering unit cases
  madhavajay
  committed
  2eabab2
- Add VNtyper large-data command plan tests
  madhavajay
  committed
  d1fdddc
- Add VNtyper expected output planning harness
  madhavajay
  committed
  c9d7ddc
- Add VNtyper external pipeline runner
  madhavajay
  committed
  49fbb68
- Wire VNtyper expected generator to pipeline runner
  madhavajay
  committed
  fc3c18f
- Tighten VNtyper full pipeline gate
  madhavajay
  committed
  2c26f98
- Add Kestrel jar build helper
  madhavajay
  committed
  ddcdfea
- Add native indexed BAM fetch support
  madhavajay
  committed
  022ff91
- Run VNtyper depth command in external pipeline
  madhavajay
  committed
  11e7ab1
- Summarize VNtyper depth output in reports
  madhavajay
  committed
  c72225d
- Resolve Kestrel jar from ignored test tools
  madhavajay
  committed
  ebb37ad
- Add VNtyper FASTQ Kestrel generation path
  madhavajay
  committed
  9448760
- Gate generated VNtyper FASTQ expected outputs
  madhavajay
  committed
  13248fa
- Add native BAM depth summary
  madhavajay
  committed
  193c5ab
- Add native BAM region slicing
  madhavajay
  committed
  355c3ac
- Mark selected native replacement milestone complete
  madhavajay
  committed
  63f5134
- Add native BAM FASTQ extraction
  madhavajay
  committed
  1c3d0fc
- Expose native samtools helpers to Python
  madhavajay
  committed
  4a8d288
- Wire native samtools into VNtyper runner
  madhavajay
  committed
  1ae2c79
- Gate native VNtyper BAM integration test
  madhavajay
  committed
  6e3f853
- Add template-based BAM FASTQ extraction
  madhavajay
  committed
  53e7bfe
- Include unmapped reads in native BAM FASTQ extraction
  madhavajay
  committed
  5b71f11
- Fix native VNtyper BAM FASTQ path
  madhavajay
  committed
  bf809eb
- Strengthen VNtyper native BAM report gate
  madhavajay
  committed
  098ba70
- Add VNtyper external BAM gate
  madhavajay
  committed
  9d21693
- Port Kestrel variant VCF normalization
  madhavajay
  committed
  f37ac80
- Add native Kestrel kmer counter
  madhavajay
  committed
  173bcdd
- Add native Kestrel active region types
  madhavajay
  committed
  cacf754
- Add native Kestrel active region detector
  madhavajay
  committed
  cb91ffe
- Add native Kestrel haplotype alignment surface
  madhavajay
  committed
  0008024
- Add native Kestrel explicit haplotype caller
  madhavajay
  committed
  d40b6f8
- Add native Kestrel kmer haplotype assembler
  madhavajay
  committed
  bcb895c
- Add native Kestrel reads to VCF path
  madhavajay
  committed
  ec81c7f
- Expose native Kestrel sequence caller to Python
  madhavajay
  committed
  68b55a7
- Add native Kestrel FASTQ caller path
  madhavajay
  committed
  84a8377
- Add Kestrel haplotype repeat controls
  madhavajay
  committed
  294cf9e
- Port Kestrel refreader fixtures to Rust
  madhavajay
  committed
  fd3966d
- Vendor Kestrel publication cases
  madhavajay
  committed
  ec49ea4
- Add Kestrel detector end-anchor controls
  madhavajay
  committed
  5995fd8
- Add Kestrel detector recovery decay
  madhavajay
  committed
  55b8f00
- Add Kestrel right-scan peak recovery
  madhavajay
  committed
  d0339da
- Add Kestrel detector scan limit
  madhavajay
  committed
  8239fa2
- Add Kestrel right anchor recovery
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  committed
  4887c6c
- Add Kestrel left peak suppression
  madhavajay
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  8f216f2
- Limit Kestrel left open scans
  madhavajay
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  40e4652
- Add Kestrel left scan recovery discard
  madhavajay
  committed
  d3c68b6
- Split Kestrel detector scan helpers
  madhavajay
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  5d7de35
- Add Kestrel ambiguous region control
  madhavajay
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  2138973
- Add Kestrel scan max gap control
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  committed
  5425823
- Add Kestrel Java parity gate
  madhavajay
  committed
  daef047
- Extend Kestrel Java parity gate
  madhavajay
  committed
  afd9f51
- Document Kestrel sparse-read parity gap
  madhavajay
  committed
  1051d9e
- Use read kmer transitions for Kestrel assembly
  madhavajay
  committed
  79aa528
- Expand Kestrel Java parity fixtures
  madhavajay
  committed
  5f65bc7
- Port Kestrel alignment weight gap limits
  madhavajay
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  72fc69c
- Port Kestrel alignment weight parser
  madhavajay
  committed
  147aea1
- Add k20 Kestrel Java parity fixture
  madhavajay
  committed
  57042d8
- Add Kestrel indel Java parity fixtures
  madhavajay
  committed
  db8c31a
- Match Kestrel mixed-depth active region DP
  madhavajay
  committed
  b62c4c2
- Expand Kestrel mixed-depth Java parity
  madhavajay
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  e16a682
- Add native Kestrel multi-reference calls
  madhavajay
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  21bfff0
- Expose multi-reference Kestrel Python wrapper
  madhavajay
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  8be6559
- Add Kestrel multi-reference Java parity
  madhavajay
  committed
  11539df
- Add Kestrel FASTA reference loader
  madhavajay
  committed
  b0ba7e3
- Wire native Kestrel into VNtyper runner
  madhavajay
  committed
  d8cdf01
- Record native Kestrel FASTQ scaling gap
  madhavajay
  committed
  c706f89
- Speed up native Kestrel kmer counting
  madhavajay
  committed
  3c6d17e
- Bound native Kestrel VNtyper runner
  madhavajay
  committed
  293c7be
- Parse named Kestrel sample columns
  madhavajay
  committed
  d8109d4
- Apply VNtyper motif filtering in port
  madhavajay
  committed
  e698f27
- Align VNtyper Kestrel report classification
  madhavajay
  committed
  dd29278
- Add native Kestrel alignment scoring
  madhavajay
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  02419a6
- Prune native Kestrel haplotypes by alignment score
  madhavajay
  committed
  872e1c0
- Record native Kestrel pruning gap
  madhavajay
  committed
  dcceff2
- Cover native Kestrel alternate haplotype pruning
  madhavajay
  committed
  14764e2
- Match Kestrel active-region overlap guard
  madhavajay
  committed
  f666d91
- Add vendored Rust bioinformatics facades
  madhavajay
  committed
  918ac3f
- Test native bcftools Python wrapper
  madhavajay
  committed
  a7d1f09
- Expand native bcftools facade
  madhavajay
  committed
  d9a93c6
- Bind native bcftools runtime methods
  madhavajay
  committed
  3d38af0
- Document BioScript library dependency graph
  madhavajay
  committed
  a8d56fa
- Document Python backend policies
  madhavajay
  committed
  56c8564
- Cover missing native Python wrappers
  madhavajay
  committed
  89b8ad8
- Add Kestrel native file runner
  madhavajay
  committed
  839d940
- Use Kestrel run facade in VNtyper port
  madhavajay
  committed
  e6bf32f
- Add minimal VNtyper port entrypoints
  madhavajay
  committed
  3d628bd
- Wire native bcftools sort into VNtyper FASTQ path
  madhavajay
  committed
  0efa1bb
- Add native bcftools switch to VNtyper BAM path
  madhavajay
  committed
  7888f42
- Wire samtools-rs into BioScript libs
  madhavajay
  committed
  4c5d58a
- Add tiny Samtools facade fixture test
  madhavajay
  committed
  1ff5f88
- Add Python native facade smoke tests
  madhavajay
  committed
  5cb5131
- Bind native Samtools methods in runtime
  madhavajay
  committed
  3f42575
- Expose familiar Samtools command facades
  madhavajay
  committed
  c2fda4e
- Update runtime TODO status
  madhavajay
  committed
  e88d6ac
- Update library support TODO status
  madhavajay
  committed
  93e60ec
- Add bcftools view facade
  madhavajay
  committed
  a0d0e5d
- Update VNtyper facade TODO status
  madhavajay
  committed
  0eeaec4
- Route pyfaidx facade through htslib-rs
  madhavajay
  committed
  12c29a0
- Expose native pyfaidx Python facade
  madhavajay
  committed
  686c24e
- Verify all-native VNtyper BAM path
  madhavajay
  committed
  64c437e
- Centralize VNtyper port config
  madhavajay
  committed
  c591290
- Cover BCFtools native error path
  madhavajay
  committed
  7e189b8
- Route pysam fetch through htslib facade
  madhavajay
  committed
  5a4b969
- Update library support TODO status
  madhavajay
  committed
  74cf060
- Add focused upstream facade parity tests
  madhavajay
  committed
  ca770ec
- Finish library support TODO
  madhavajay
  committed
  7208235
- Reset TODO for native VNtyper port
  madhavajay
  committed
  981b8b3
- Establish native VNtyper baseline gates
  madhavajay
  committed
  a4f5d26
- Add runnable VNtyper BioScript plan
  madhavajay
  committed
  2e8567b
- Add native FASTQ VNtyper parity gate
  madhavajay
  committed
  b2d3742
- Add VNtyper native facade test
  madhavajay
  committed
  4da9c0f
- Add VNtyper runtime program test
  madhavajay
  committed
  23d41c8
- Add VNtyper FASTQ BioScript plan
  madhavajay
  committed
  b8a2091
- Split all-native BAM parity prerequisites
  madhavajay
  committed
  ad6cd22
- Record FASTQ native parity gap
  madhavajay
  committed
  dbf94f3
- Add VNtyper VCF parser tests
  madhavajay
  committed
  b911d76
- Tighten VNtyper parity skip gates
  madhavajay
  committed
  8d31f5c
- Mark tool planners as planning APIs
  madhavajay
  committed
  fcce287
- Record BCFtools view filter decision
  madhavajay
  committed
  e276c62
- Record FASTQ fixture expectation status
  madhavajay
  committed
  86a3901
- Record VNtyper HTML report gate
  madhavajay
  committed
  d2db51e
- Fix native samtools FASTQ singleton parity
  madhavajay
  committed
  1fcb4ee
- Record VNtyper output parity deltas
  madhavajay
  committed
  27f515f
- Reconfirm native FASTQ Kestrel parity gap
  madhavajay
  committed
  4d5ed5c
- Add Kestrel VNtyper FASTQ parity gate
  madhavajay
  committed
  39e0e33
- Record native FASTQ execution path
  madhavajay
  committed
  21dcd86
- Tighten VNtyper upstream test map
  madhavajay
  committed
  fdd58cb
- Default matching runtime tool calls to native facades
  madhavajay
  committed
  01dbc86
- Default samtools runtime calls to native facades
  madhavajay
  committed
  ff8f9d2
- Add native Kestrel runtime execution
  madhavajay
  committed
  dec79f9
- Record facade replacement regression coverage
  madhavajay
  committed
  26f92e6
- Run VNtyper FASTQ BioScript through native facades
  madhavajay
  committed
  180b02d
- Record VNtyper scaffold test retention
  madhavajay
  committed
  2263b6c
- Record native FASTQ runtime coverage in VNtyper map
  madhavajay
  committed
  2843e4a
- Add VNtyper Kestrel call rows to vcf facade
  madhavajay
  committed
  97df779
- Build VNtyper report JSON from vcf facade
  madhavajay
  committed
  054878b
- Materialize VNtyper Kestrel TSV in runtime slice
  madhavajay
  committed
  850d3db
- Add native BAM VNtyper runtime slice
  madhavajay
  committed
  bc88c56
- Thread VNtyper report context through vcf facade
  madhavajay
  committed
  03f9383
- Promote VNtyper BAM entry point to native runtime
  madhavajay
  committed
  aadef16
- Close VNtyper syntax and upstream map TODOs
  madhavajay
  committed
  d3e4af2
- Refresh native FASTQ parity blocker evidence
  madhavajay
  committed
  92f3f7e
- Record Kestrel engine FASTQ parity failure
  madhavajay
  committed
  6913323
- Parameterize VNtyper Kestrel runtime settings
  madhavajay
  committed
  70e4b1c
- Document native FASTQ false-positive diagnostics
  madhavajay
  committed
  0393450
- Add native FASTQ parity failure context
  madhavajay
  committed
  99c8f1d
- Add normalized FASTQ output parity fingerprints
  madhavajay
  committed
  5d381a8
- Audit remaining TODO parity blockers
  madhavajay
  committed
  9b93635
- Document VNtyper Kestrel limit parity gap
  madhavajay
  committed
  e096caa
- Add normalized BAM output parity gate
  madhavajay
  committed
  f8a56f7
- Match VNtyper motif filters in vcf facade
  madhavajay
  committed
  5fe688d
- Record Kestrel parity diff examples
  madhavajay
  committed
  c69c318
- Document Kestrel graph traversal parity gap
  madhavajay
  committed
  2a5cee5
- Record discarded Kestrel graph traversal attempt
  madhavajay
  committed
  40f86d1
- Document Kestrel parity artifact retention
  madhavajay
  committed
  9ef3332
- Record VNtyper Kestrel delta summary
  madhavajay
  committed
  07758da
- Document Kestrel parity limit overrides
  madhavajay
  committed
  01b4f69
- Record upstream-limit Kestrel timeout
  madhavajay
  committed
  6ae6abb
- Document Kestrel VNtyper parity progress
  madhavajay
  committed
  7a5ea8f
- Update fix-kestrel.md with kmercount filter findings
  madhavajay
  committed
  f9aecf4
- Update fix-kestrel.md with progress summary table and verification notes
  madhavajay
  committed
  cfeedf7
- Add break-cause counter findings and next-step hypothesis to fix-kestrel.md
  madhavajay
  committed
  c1a04b1
- Record seq_limit knob experiment results in fix-kestrel.md
  madhavajay
  committed
  37a52c4
- Document diagnostic test findings and next-step options
  madhavajay
  committed
  9dbb2a7
- Document haplotype_built and min_depth investigation in fix-kestrel.md
  
  madhavajay
  and
  claude
  committed
  5672c9c
- Document iter 25-40 cycle pattern in J-R outer iters
  
  madhavajay
  and
  claude
  committed
  48280a7
- Record aggressive dedup experiment and session summary
  
  madhavajay
  and
  claude
  committed
  799d335
- Record shape dedup experiment and exhaustive knob inventory
  madhavajay
  committed
  fac2b16
- Record cap-sweep diagnostic: bug exists at every cap level
  
  madhavajay
  and
  claude
  committed
  26cafc8
- Pinpoint iter 4 divergence with Java instrumentation + Rust restore trace
  
  madhavajay
  and
  claude
  committed
  ad522bb
- Trace shows Java's iter 4 = Rust's iter 6 (G-alt restore)
  
  madhavajay
  and
  claude
  committed
  e2d43f1
- ROOT CAUSE FIX: Java's nState accounting (save -1 on evict, NOT on pop)
  
  madhavajay
  and
  claude
  committed
  95968c2
- Analyze post-fix parity gap: 1028 missing has DP value differences
  
  madhavajay
  and
  claude
  committed
  7d1eb7c
- Session conclusion: root cause solved, 78% of parity gap closed
  madhavajay
  committed
  434e1b6
- Consolidate session summary in fix-kestrel.md
  
  madhavajay
  and
  claude
  committed
  b077aad
- Advance kestrel-rs to merged parity fix; add APOL1 pysam proof
  
  madhavajay
  and
  claude
  committed
  ccca069
- TODO: set test-vntyper.sh Java<->Rust parity as current priority
  
  madhavajay
  and
  claude
  committed
  de8f672
- test-vntyper.sh: Java↔Rust VNtyper output parity tool
  
  madhavajay
  and
  claude
  committed
  76a1c1a
- VNtyper: all-fixture upstream correctness + Java↔Rust parity
  
  madhavajay
  and
  claude
  committed
  5a67eb6
- Regenerate rust/Cargo.lock after merging origin/main
  
  madhavajay
  and
  claude
  committed
  7993469
- Update VNtyper Rust tests for kestrel-rs Java-parity output
  
  madhavajay
  and
  claude
  committed
  dc3d71b
- Add VNtyper advanced-assay example + runtime support for native assays
  
  madhavajay
  and
  claude
  committed
  96483cf
- updating libs
  madhavajay
  committed
  b8b19bb
- adding repoverse
  madhavajay
  committed
  04dba67
- remove
  madhavajay
  committed
  b0932e0
- adding repoverse
  madhavajay
  committed
  7e89281
- updating samtools
  madhavajay
  committed
  c59bb3f
- adding extra noodles checkout
  madhavajay
  committed
  381997e
- updating submodule
  madhavajay
  committed
  ae29304
- fixing path
  madhavajay
  committed
  5ec071f
- fixes
  madhavajay
  committed
  fc18e99
- Merge remote-tracking branch 'origin/main' into madhava/libs
  madhavajay
  committed
  69beb85
- Bump htslib-rs/bcftools-rs/samtools-rs to current main; cargo fmt
  madhavajay
  committed
  8e65283
- Untrack macOS-only cargo env; fix clippy::pedantic warnings
  madhavajay
  committed
  3e4b32c
Commits on Jun 1, 2026
- removing c dep
  madhavajay
  committed
  1e01480
Commits on Jun 3, 2026
- Use virtual runtime paths in wasm
  madhavajay
  committed
  ebb60d5

Commits

Commits on May 27, 2026