v2.10.2: surface stale-MD warning (extract + call)

What's new

Both fiberhmm-extract and fiberhmm-call --mode daf now print a clear note when they detect MD tags that disagree with their CIGAR (common on consensus BAMs where MD is stale after CIGAR was recomputed). Example:

NOTE: 11/20 of the sniffed reads have MD tags that
disagree with their CIGAR (typical of consensus BAMs where
MD was inherited stale after CIGAR was recomputed).
These reads will be SKIPPED for --deam only; other tracks
extract normally. The reads themselves are not corrupt --
the CIGAR is still correct, only the MD annotation is stale.
To recover --deam calls for those reads, regenerate MD with:
  samtools calmd -b aligned.bam ref.fa > fixed.bam

v2.10.1 silently skipped those reads. That left users unsure whether their data was corrupt and whether anything had been dropped. v2.10.2 makes it explicit, up-front, and actionable.

Warning only fires when --deam actually depends on MD (no R/Y in sequence, no MM/ML dU code, no --reference on the call side) AND at least one sniffed read has the mismatch. Free — reuses the v2.10.1 validator. No code path changes beyond printing the note.

Install

pip install --upgrade fiberhmm