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v2.10.3: README promotes one-step DAF pipeline (docs-only)
Docs-only release
Three README updates so the documentation matches the v2.10.0+ reality:
-
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
-
fiberhmm-daf-encodeCLI reference — added an "Optional in v2.10.0+" banner. The tool still exists and still works; most users just don't need it anymore. -
Tag reference — clarified that
st:Zis written only byfiberhmm-daf-encode(the two-pass path), not byfiberhmm-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