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FiberHMM 2.16.8

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@mtcicero26 mtcicero26 released this 25 Aug 02:08
· 377 commits to main since this release
v2.16.8
2e3262f

FiberHMM 2.16.8

This release adds an integrated, nondestructive DAF-seq cleanup and QC path.

DddA/DddB call workflow

  • File-based fiberhmm-call now runs endpoint-constrained deamination-
    fingerprint duplicate detection automatically before footprint calling.
  • Integrated deduplication retains every read by default and marks copies with
    SAM flag 0x400 plus di/ds cluster tags. Use --dedup-collapse only to
    request destructive removal, or --no-dedup to disable detection.
  • Adequately covered DddA/DddB samples are screened automatically for recurrent
    C→T/G→A SNPs after duplicate marking and before the HMM. Low-depth samples
    skip the full caller, and all thresholds remain user-configurable.
  • SNP calls require fraction, depth, and alternate-fiber support independently
    in both conversion-direction classes. The mask affects HMM observations only;
    read sequence and MD tags are preserved.
  • Bounded assay-matched QC runs after file-based calls by default. Disable it
    with --no-qc.

New QC and SNP tools

  • fiberhmm-qc accepts one or multiple BAMs and produces per-sample reports
    plus a combined comparison dashboard.
  • QC includes signal-rate distributions and empirical safe zones,
    nucleosome-scale phasing, nucleosome/TF footprint-size distributions,
    example molecules, duplicate statistics, SNP diagnostics, and terminal
    PASS/WARN/FAIL scores.
  • Sampling is deterministic and bounded (2,000 reads by default), avoiding
    full rescans of very large BAMs.
  • Every plot is emitted as PNG and as a vector PDF with editable text for
    Illustrator.
  • Packaged reference data contain aggregate curves and anonymized visual
    exemplars only. Control BAMs, read sequences, and genomic coordinates are not
    redistributed; provenance is documented in the package.
  • fiberhmm-daf-snps emits BED, VCF, JSON, a mismatch landscape, an amplicon
    table, and amplicon coverage/coordinate/SNP-location maps.

FiberBrowser interoperability

  • fiberhmm-extract now appends isDuplicate to BED/bigBed records so
    FiberBrowser v2.17.1 can hide marked PCR copies by default and reveal them
    interactively.

Validation

  • Complete clean-candidate suite: 541 passed, 3 skipped.
  • Focused dedup/SNP/QC/extraction suite: 107 passed.
  • Wheel and source distribution built successfully with all QC assets and new
    command entry points included.

Recommended companion release: FiberBrowser v2.17.1.

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