vafator 3.0.0

Performance

~13x runtime improvement over v2 on a 292K variant VCF (SEQC2 WES WES_EA_1, 5.5 hours → 23 minutes with 4 cores).

Streaming pileup iterator — replaced per-variant bam.pileup() calls with a single pileup iterator per chromosome per BAM. This eliminates the dominant source of overhead (repeated pysam pileup object construction and destruction) and reduces runtime ~4.4x on its own.
Power calculation caching — _calculate_k and calculate_expected_vaf results are now cached per depth value and per (sample, chrom, pos) respectively, avoiding redundant scipy.stats.binom calls across variants with identical coverage.
Rank sum test early exit — calculate_rank_sum_test now returns nan immediately when either distribution is empty, skipping unnecessary scipy.stats.ranksums calls.
Chromosome-level parallelization — added --num-processes flag to distribute chromosomes across worker processes using ProcessPoolExecutor. Each worker opens its own BAM readers independently, avoiding shared state issues.

Python upgraded to 3.11
pysam pinned to ==0.21.0 — versions 0.22+ have a regression where query_qualities returns incorrect values.

--include-ambiguous-bases renamed to --exclude-ambiguous-bases — ambiguous bases (N and all IUPAC codes) are now included in depth of coverage by default. To restore the old behaviour of excluding them, pass --exclude-ambiguous-bases. This flag is inverted from the previous version.
Zero-coverage variants — _bq, _mq, _pos annotations for variants with zero coverage previously reported nan; they now report 0.0. This affects a small number of variants (9/292,009 in the tested VCF).

VafatorVariant replaced by VariantRecord — the test utility class VafatorVariant (from vafator.tests.utils) is now a thin factory function returning a VariantRecord.
Async VCF writing removed — the @background / asyncio / time.sleep(2) writing pattern was causing missing variants in the output. Replaced with synchronous batch writing.
Type hints and docstrings added throughout annotator.py, pileups.py, and pileup_utils.py.