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OpenMined / bioscript Public

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Madhava/libs#68

Open

madhavajay wants to merge 219 commits into

mainOpenMined/bioscript:mainfrom

madhava/libsOpenMined/bioscript:madhava/libsCopy head branch name to clipboard

Conversation Commits219 (219)Checks Files changed

Open

Madhava/libs#68
madhavajay wants to merge 219 commits into
mainfrom
madhava/libs

Commits

Commits on May 27, 2026

Add BioScript library shim infrastructure
madhavajay
committed
Add VNtyper BioScript port scaffolding
madhavajay
committed
Add bcftools wrapper surface
madhavajay
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Gate VNtyper integration data tests
madhavajay
committed
Split runtime tool method bindings
madhavajay
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Document VNtyper upstream inventory
madhavajay
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Add VNtyper region helpers
madhavajay
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Add VNtyper command planner
madhavajay
committed
Mark VNtyper port skeleton milestone
madhavajay
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Add optional VNtyper upstream scoring parity test
madhavajay
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Record VNtyper port decisions
madhavajay
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Add VNtyper expected fixture outputs
madhavajay
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Expand VNtyper structured report JSON
madhavajay
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Add VNtyper adVNTR report fields
madhavajay
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Add initial VNtyper HTML report
madhavajay
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Record tool command planning timings
madhavajay
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Triage VNtyper optional modules
madhavajay
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Document Kestrel native port spike
madhavajay
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Gate VNtyper full pipeline prerequisites
madhavajay
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Add interactive VNtyper report controls
madhavajay
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Gate upstream VNtyper reference tests
madhavajay
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Add VNtyper IGV report session
madhavajay
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Port VNtyper scoring unit cases
madhavajay
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Port VNtyper flagging unit cases
madhavajay
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Port VNtyper motif filtering unit cases
madhavajay
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Add VNtyper large-data command plan tests
madhavajay
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Add VNtyper expected output planning harness
madhavajay
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Add VNtyper external pipeline runner
madhavajay
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Wire VNtyper expected generator to pipeline runner
madhavajay
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Tighten VNtyper full pipeline gate
madhavajay
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Add Kestrel jar build helper
madhavajay
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Add native indexed BAM fetch support
madhavajay
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Run VNtyper depth command in external pipeline
madhavajay
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Summarize VNtyper depth output in reports
madhavajay
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Resolve Kestrel jar from ignored test tools
madhavajay
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Add VNtyper FASTQ Kestrel generation path
madhavajay
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Gate generated VNtyper FASTQ expected outputs
madhavajay
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Add native BAM depth summary
madhavajay
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Add native BAM region slicing
madhavajay
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Mark selected native replacement milestone complete
madhavajay
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Add native BAM FASTQ extraction
madhavajay
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Expose native samtools helpers to Python
madhavajay
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Wire native samtools into VNtyper runner
madhavajay
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Gate native VNtyper BAM integration test
madhavajay
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Add template-based BAM FASTQ extraction
madhavajay
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Include unmapped reads in native BAM FASTQ extraction
madhavajay
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Fix native VNtyper BAM FASTQ path
madhavajay
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Strengthen VNtyper native BAM report gate
madhavajay
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Add VNtyper external BAM gate
madhavajay
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Port Kestrel variant VCF normalization
madhavajay
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Add native Kestrel kmer counter
madhavajay
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Add native Kestrel active region types
madhavajay
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Add native Kestrel active region detector
madhavajay
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Add native Kestrel haplotype alignment surface
madhavajay
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Add native Kestrel explicit haplotype caller
madhavajay
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Add native Kestrel kmer haplotype assembler
madhavajay
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Add native Kestrel reads to VCF path
madhavajay
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Expose native Kestrel sequence caller to Python
madhavajay
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Add native Kestrel FASTQ caller path
madhavajay
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Add Kestrel haplotype repeat controls
madhavajay
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Port Kestrel refreader fixtures to Rust
madhavajay
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Vendor Kestrel publication cases
madhavajay
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Add Kestrel detector end-anchor controls
madhavajay
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Add Kestrel detector recovery decay
madhavajay
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Add Kestrel right-scan peak recovery
madhavajay
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Add Kestrel detector scan limit
madhavajay
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Add Kestrel right anchor recovery
madhavajay
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Add Kestrel left peak suppression
madhavajay
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Limit Kestrel left open scans
madhavajay
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Add Kestrel left scan recovery discard
madhavajay
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Split Kestrel detector scan helpers
madhavajay
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Add Kestrel ambiguous region control
madhavajay
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Add Kestrel scan max gap control
madhavajay
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Add Kestrel Java parity gate
madhavajay
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Extend Kestrel Java parity gate
madhavajay
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Document Kestrel sparse-read parity gap
madhavajay
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Use read kmer transitions for Kestrel assembly
madhavajay
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Expand Kestrel Java parity fixtures
madhavajay
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Port Kestrel alignment weight gap limits
madhavajay
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Port Kestrel alignment weight parser
madhavajay
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Add k20 Kestrel Java parity fixture
madhavajay
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Add Kestrel indel Java parity fixtures
madhavajay
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Match Kestrel mixed-depth active region DP
madhavajay
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Expand Kestrel mixed-depth Java parity
madhavajay
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Add native Kestrel multi-reference calls
madhavajay
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Expose multi-reference Kestrel Python wrapper
madhavajay
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Add Kestrel multi-reference Java parity
madhavajay
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Add Kestrel FASTA reference loader
madhavajay
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Wire native Kestrel into VNtyper runner
madhavajay
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Record native Kestrel FASTQ scaling gap
madhavajay
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Speed up native Kestrel kmer counting
madhavajay
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Bound native Kestrel VNtyper runner
madhavajay
committed
Parse named Kestrel sample columns
madhavajay
committed
Apply VNtyper motif filtering in port
madhavajay
committed
Align VNtyper Kestrel report classification
madhavajay
committed
Add native Kestrel alignment scoring
madhavajay
committed
Prune native Kestrel haplotypes by alignment score
madhavajay
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Record native Kestrel pruning gap
madhavajay
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Cover native Kestrel alternate haplotype pruning
madhavajay
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Match Kestrel active-region overlap guard
madhavajay
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Add vendored Rust bioinformatics facades
madhavajay
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Test native bcftools Python wrapper
madhavajay
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Expand native bcftools facade
madhavajay
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Bind native bcftools runtime methods
madhavajay
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Document BioScript library dependency graph
madhavajay
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Document Python backend policies
madhavajay
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Cover missing native Python wrappers
madhavajay
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Add Kestrel native file runner
madhavajay
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Use Kestrel run facade in VNtyper port
madhavajay
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Add minimal VNtyper port entrypoints
madhavajay
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Wire native bcftools sort into VNtyper FASTQ path
madhavajay
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Add native bcftools switch to VNtyper BAM path
madhavajay
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Wire samtools-rs into BioScript libs
madhavajay
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Add tiny Samtools facade fixture test
madhavajay
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Add Python native facade smoke tests
madhavajay
committed
Bind native Samtools methods in runtime
madhavajay
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Expose familiar Samtools command facades
madhavajay
committed
Update runtime TODO status
madhavajay
committed
Update library support TODO status
madhavajay
committed
Add bcftools view facade
madhavajay
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Update VNtyper facade TODO status
madhavajay
committed
Route pyfaidx facade through htslib-rs
madhavajay
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Expose native pyfaidx Python facade
madhavajay
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Verify all-native VNtyper BAM path
madhavajay
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Centralize VNtyper port config
madhavajay
committed
Cover BCFtools native error path
madhavajay
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Route pysam fetch through htslib facade
madhavajay
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Update library support TODO status
madhavajay
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Add focused upstream facade parity tests
madhavajay
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Finish library support TODO
madhavajay
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Reset TODO for native VNtyper port
madhavajay
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Establish native VNtyper baseline gates
madhavajay
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Add runnable VNtyper BioScript plan
madhavajay
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Add native FASTQ VNtyper parity gate
madhavajay
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Add VNtyper native facade test
madhavajay
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Add VNtyper runtime program test
madhavajay
committed
Add VNtyper FASTQ BioScript plan
madhavajay
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Split all-native BAM parity prerequisites
madhavajay
committed
Record FASTQ native parity gap
madhavajay
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Add VNtyper VCF parser tests
madhavajay
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Tighten VNtyper parity skip gates
madhavajay
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Mark tool planners as planning APIs
madhavajay
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Record BCFtools view filter decision
madhavajay
committed
Record FASTQ fixture expectation status
madhavajay
committed
Record VNtyper HTML report gate
madhavajay
committed
Fix native samtools FASTQ singleton parity
madhavajay
committed
Record VNtyper output parity deltas
madhavajay
committed
Reconfirm native FASTQ Kestrel parity gap
madhavajay
committed
Add Kestrel VNtyper FASTQ parity gate
madhavajay
committed
Record native FASTQ execution path
madhavajay
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Tighten VNtyper upstream test map
madhavajay
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Default matching runtime tool calls to native facades
madhavajay
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Default samtools runtime calls to native facades
madhavajay
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Add native Kestrel runtime execution
madhavajay
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Record facade replacement regression coverage
madhavajay
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Run VNtyper FASTQ BioScript through native facades
madhavajay
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Record VNtyper scaffold test retention
madhavajay
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Record native FASTQ runtime coverage in VNtyper map
madhavajay
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Add VNtyper Kestrel call rows to vcf facade
madhavajay
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Build VNtyper report JSON from vcf facade
madhavajay
committed
Materialize VNtyper Kestrel TSV in runtime slice
madhavajay
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Add native BAM VNtyper runtime slice
madhavajay
committed
Thread VNtyper report context through vcf facade
madhavajay
committed
Promote VNtyper BAM entry point to native runtime
madhavajay
committed
Close VNtyper syntax and upstream map TODOs
madhavajay
committed
Refresh native FASTQ parity blocker evidence
madhavajay
committed
Record Kestrel engine FASTQ parity failure
madhavajay
committed
Parameterize VNtyper Kestrel runtime settings
madhavajay
committed
Document native FASTQ false-positive diagnostics
madhavajay
committed
Add native FASTQ parity failure context
madhavajay
committed
Add normalized FASTQ output parity fingerprints
madhavajay
committed
Audit remaining TODO parity blockers
madhavajay
committed
Document VNtyper Kestrel limit parity gap
madhavajay
committed
Add normalized BAM output parity gate
madhavajay
committed
Match VNtyper motif filters in vcf facade
madhavajay
committed
Record Kestrel parity diff examples
madhavajay
committed
Document Kestrel graph traversal parity gap
madhavajay
committed
Record discarded Kestrel graph traversal attempt
madhavajay
committed
Document Kestrel parity artifact retention
madhavajay
committed
Record VNtyper Kestrel delta summary
madhavajay
committed
Document Kestrel parity limit overrides
madhavajay
committed
Record upstream-limit Kestrel timeout
madhavajay
committed
Document Kestrel VNtyper parity progress
madhavajay
committed
Update fix-kestrel.md with kmercount filter findings
madhavajay
committed
Update fix-kestrel.md with progress summary table and verification notes
madhavajay
committed
Add break-cause counter findings and next-step hypothesis to fix-kestrel.md
madhavajay
committed
Record seq_limit knob experiment results in fix-kestrel.md
madhavajay
committed
Document diagnostic test findings and next-step options
madhavajay
committed
Document haplotype_built and min_depth investigation in fix-kestrel.md

madhavajay
and
claude
committed
Document iter 25-40 cycle pattern in J-R outer iters

madhavajay
and
claude
committed
Record aggressive dedup experiment and session summary

madhavajay
and
claude
committed
Record shape dedup experiment and exhaustive knob inventory
madhavajay
committed
Record cap-sweep diagnostic: bug exists at every cap level

madhavajay
and
claude
committed
Pinpoint iter 4 divergence with Java instrumentation + Rust restore trace

madhavajay
and
claude
committed
Trace shows Java's iter 4 = Rust's iter 6 (G-alt restore)

madhavajay
and
claude
committed
ROOT CAUSE FIX: Java's nState accounting (save -1 on evict, NOT on pop)

madhavajay
and
claude
committed
Analyze post-fix parity gap: 1028 missing has DP value differences

madhavajay
and
claude
committed
Session conclusion: root cause solved, 78% of parity gap closed
madhavajay
committed
Consolidate session summary in fix-kestrel.md

madhavajay
and
claude
committed
Advance kestrel-rs to merged parity fix; add APOL1 pysam proof

madhavajay
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claude
committed
TODO: set test-vntyper.sh Java<->Rust parity as current priority

madhavajay
and
claude
committed
test-vntyper.sh: Java↔Rust VNtyper output parity tool

madhavajay
and
claude
committed
VNtyper: all-fixture upstream correctness + Java↔Rust parity

madhavajay
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claude
committed
Regenerate rust/Cargo.lock after merging origin/main

madhavajay
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claude
committed
Update VNtyper Rust tests for kestrel-rs Java-parity output

madhavajay
and
claude
committed
Add VNtyper advanced-assay example + runtime support for native assays

madhavajay
and
claude
committed
updating libs
madhavajay
committed
adding repoverse
madhavajay
committed
remove
madhavajay
committed
adding repoverse
madhavajay
committed
updating samtools
madhavajay
committed
adding extra noodles checkout
madhavajay
committed
updating submodule
madhavajay
committed
fixing path
madhavajay
committed
fixes
madhavajay
committed
Merge remote-tracking branch 'origin/main' into madhava/libs
madhavajay
committed
Bump htslib-rs/bcftools-rs/samtools-rs to current main; cargo fmt
madhavajay
committed
Untrack macOS-only cargo env; fix clippy::pedantic warnings
madhavajay
committed

Commits on Jun 1, 2026

removing c dep
madhavajay
committed

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