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v2.10.3: README promotes one-step DAF pipeline (docs-only)

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@mtcicero26 mtcicero26 released this 23 Apr 17:01
· 491 commits to main since this release

Docs-only release

Three README updates so the documentation matches the v2.10.0+ reality:

  1. Streaming Pipelines section — replaced the stale DAF example (minimap2 | daf-encode | apply) with the one-pass form:

    minimap2 --MD -a ref.fa reads.fq | samtools view -b | \
        fiberhmm-call --mode daf --enzyme dddb -i - -o - | \
        ft fire - final.bam
  2. fiberhmm-daf-encode CLI reference — added an "Optional in v2.10.0+" banner. The tool still exists and still works; most users just don't need it anymore.

  3. Tag reference — clarified that st:Z is written only by fiberhmm-daf-encode (the two-pass path), not by fiberhmm-call --mode daf (the one-pass path derives strand internally from MD).

No code changes. No behavior changes. 292 tests still pass.

Install

pip install --upgrade fiberhmm