6.3.0 — configurable observe_molecules; secondary/supplementary filters fixed

✨ Added

• observe_molecules() takes the settings it actually uses. New keyword arguments
  filters, quality, alignment, umi_tag, threads, apply_baq and library_type
  sit alongside the existing config=, which keeps working; an individual argument
  overrides the matching config field.

  Previously the only way to change a setting was to build a whole GbcmsDnaConfig, whose
  four required fields — variant_file, bam_files, reference_fasta, output — have
  zero overlap with the seven this entry point reads. Two of them must name files that
  exist on disk. So adjusting one filter meant fabricating an output directory and a variant
  path that are never touched: paths that look load-bearing and are not.

  Found by the first real consumer (mulligan) needing a non-default read filter.

  umi_tag is the one argument where None is an explicit choice rather than an omission —
  it means "group by read pair, not UMI family" and overrides config accordingly. Every
  other argument treats None as "not supplied". Without that distinction, a caller passing
  umi_tag=None alongside a config that sets one would silently inherit it and change what
  counts as a molecule.

🐛 Fixed

• --filter-secondary and --filter-supplementary now change the result when turned
  off. They previously could not change any output: an unconditional skip in the
  counting loop discarded those records before fragment evidence, regardless of the
  flags. Measured across all six read filters on real MSK-ACCESS data, these were the only
  two that did nothing (duplicates, improper_pair and indel all worked).
  (#82)

  Default runs are byte-identical — both filters still default to on, so such records
  never reach the cache. Verified on real data: total depth unchanged at 1202 across 40
  loci, and binned↔legacy parity holds.

  Turning a filter off now admits those records to fragment-level evidence
  (dpf/rdf/adf) and to the per-molecule observation export. They still never
  contribute to read-level dp/rd/ad: a supplementary shares a QNAME with its primary
  and is the same physical read, so counting both would report depth 2 where one read
  exists. Fragments are immune either way — hash_molecule keys on QNAME, so a primary and
  its supplementary collapse into one.

  What this fixes concretely: a locus reached only by a supplementary segment used to
  report dpf=0 — not a filtered read but a wrong answer, since a molecule demonstrably
  covers it. That is what made a molecule spanning a large deletion invisible to
  cross-locus phasing.

  New consequence to be aware of: with the filter off, an admitted supplementary raises
  dpf while leaving dp unchanged, so the two stop moving together. The observation
  export reconciles with dpf, and that invariant is verified under both settings.