Move to sample ids - #428
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Replace the index-centric sample-selection surface with a
sample-ID-centric one. VczReader.set_samples now takes sample IDs:
set_samples(sample_ids, *, complement=False, ignore_missing_samples=False)
resolving names to indexes internally (the reader already owns
raw_sample_ids). A lower-level set_sample_indexes keeps the raw-index
entry point for callers that work in indexes.
This lets vcztools/samples.py be removed: SampleChunkPlan and the
chunk-plan builder move into retrieval.py (build_sample_chunk_plan,
renamed to avoid colliding with regions.build_chunk_plan), the
name-to-index resolver becomes retrieval._resolve_sample_names, and the
samples-file reader moves to cli._read_samples_file. The CLI now calls
set_samples directly and rejects an empty resolved set via
reader.sample_ids.
Tests for the relocated helpers move to test_retrieval.py /
test_cli.py; index-based set_samples calls become set_sample_indexes.
The non-null sample index array is internal machinery (num_null_samples, the bcftools-view output-column remap, and the full-sample filter plan) rather than part of the reader's selection API, which is now ID-centric. Rename it to a private cached property and drop the public docs that illustrated building index selections from it.
Match the "indexes" spelling used elsewhere (set_sample_indexes, sample_indexes).
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