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Merge dev changes - #39

Merged

DonFreed merged 65 commits into

mainfrom

dev

Oct 2, 2026

Merged

Merge dev changes#39
DonFreed merged 65 commits into
mainfrom
dev

Commits on Jul 24, 2026
- Pass the `--pangenome_contig_prefix` to `PangenomeSV`.
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Commits on Aug 12, 2026
- Fix shell-pipeline correctness bugs and size internal pipes natively
  
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- Rework the DAG/scheduler/executor engine layer
  
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- Fix BasePipeline lifecycle issues
  
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Commits on Aug 13, 2026
- Trim unused engine functionality and condense comments
  
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- Merge pull request #30 from Sentieon/engine-updates
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- Add a per-run log directory with run.log and command.txt
  
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Commits on Aug 14, 2026
- Give jobs a task name and a unique, human-readable job id
  
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- Capture each process's output to per-task log files
  
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- Merge pull request #31 from Sentieon/log-restructure
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- Fix log-directory setup ordering, id sanitization, and verbosity flags
  
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- Record per-process rusage by owning the child reap
  
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- Report per-process rusage in the run logs
  
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- Test rusage capture and the per-process metrics report
  
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- Tear down children when the run loop fails; make the wait pool tunable
  
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- Merge pull request #32 from Sentieon/log-metrics
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Commits on Aug 15, 2026
- Add the hybrid-pangenome pipeline
  
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Commits on Aug 16, 2026
- Support aligned short-read and unaligned long-read input in hybrid-pangenome
  
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- Sort SV update regions in reference contig order
  
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- Thread the pangenome contig prefix through all graph consumers
  
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- Harden input readgroup validation and the KMC patch check
  
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Commits on Aug 17, 2026
- Sort the HybridStage1 hap_bam output explicitly
  
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- Remove the temporary directory when a sentieon-pangenome run fails
  
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- Revert the k-mer count check in check_kmc_patch
  
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Commits on Aug 18, 2026
- Increment version
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- Use the SENTIEON_VERSION repo variable in CI-smoke
  
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- Merge pull request #33 from Sentieon/hybrid-pangenome
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Commits on Aug 19, 2026
- Write per-process and per-job metrics tables to the log directory
  
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Commits on Aug 22, 2026
- Run pangenome metrics on the bwa alignment only
  
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Commits on Aug 31, 2026
- Update the pangenome AD and DP counts from SAD or LAD
  
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Commits on Sep 1, 2026
- Support the new CNVscope syntax from release 202503.04
  
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Commits on Sep 2, 2026
- Emit --interval_padding only when it is set
  
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- Add the stage building blocks
  
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- Move CNV calling and ploidy estimation into stages
  
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- Move duplicate marking and metrics into stages
  
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- Move small-variant calling into stages
  
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- Insert the hybrid calling jobs directly into the DAG
  
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- Insert the long-read calling jobs directly into the DAG
  
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- Move alignment and read extraction into stages
  
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- Use the shared version-check and required-argument helpers
  
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- Remove unused helpers
  
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Commits on Sep 4, 2026
- Simplify the stages after review
  
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- Move short-read preprocessing, mosdepth and LongReadSV into stages
  
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- Make the hybrid pipeline a direct BasePipeline subclass
  
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- Drop the attribute renames from validate()
  
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- Update the require_versions docstring
  
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- Default the hybrid pipeline's minimap2 arguments to -YL
  
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- Run the pangenome pipeline through BasePipeline.main
  
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- Collect the transfer inputs with TransferConfig.from_pipeline
  
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- Let the hybrid pangenome pipeline use LongReadSVStage
  
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Commits on Sep 5, 2026
- Skip CNV calling in the hybrid smoke tests
  
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- Merge pull request #36 from Sentieon/code-refactor
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- Write CRAM output with the default util sort arguments
  
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- Pass --dump_probes to CNVscope
  
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Commits on Sep 8, 2026
- Extract the pangenome FASTA with vg paths on non-GRCh38 references
  
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- Add segdup, ExpansionHunter, T1K and pangenome CNV stages
  
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- Compose the dnascope-pangenome callers from the shared stages
  
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- Validate the optional callers and estimate ploidy in hybrid-pangenome
  
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- Call CNVs, repeat expansions and segdups in the hybrid-pangenome second DAG
  
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- Merge pull request #37 from Sentieon/hybrid-pangenome-callers
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- Drop the path selector from the vg paths gfa2fa fallback
  
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- Import SEGDUP_MIN_VERSIONS from stages.segdup in the Dockerfile
  
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Commits on Sep 12, 2026
- Detect the pangenome reference from the GBZ metadata
  
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- Check pop VCF contig lengths against the reference for any backbone
  
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Commits on Sep 13, 2026
- Merge pull request #38 from Sentieon/gbz-name-validation
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  4756e9e

Commits

Commits on Jul 24, 2026

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