[NicoDeVeaux]

fix(bam): per-reference CRAM fetch keeps only that reference's records

For PR #118, stacked on fix/pr118-unmapped-sweep (base #118 head 0b00cf1). Found while testing that branch; not one of the review's findings.

What

IndexedReader::fetch(tid) on a CRAM now keeps only records whose reference sequence ID is tid.

Why

noodles' CRAM query (noodles-cram 0.94.0, io/reader/query.rs) selects containers through the index but then filters records by interval only, not by reference. In a multi-reference slice (htslib can write these when references have few records, such as many small contigs; --output-fmt-option multi_seq_per_slice=1 forces one) a per-reference fetch over the whole-reference interval also returns the other references' records. On the parallel path each such record is counted once per reference fetch.

Input: tests/data/unmapped_sweep/multi_ref_slice.cram (six records, chr1/chr2 and two unplaced, in one slice; samtools 1.22.1), --reference sweep.fa:

build	-t 1 in total	-t 4 in total
samtools 1.22.1 flagstat	6 + 0
main bea5571 (htslib)	6 + 0	6 + 0
#118 0b00cf1	6 + 0	11 + 0
fix/pr118-unmapped-sweep	6 + 0	10 + 0
this branch	6 + 0	6 + 0

The per-reference CRAMs (single_ref_slices.cram) give 6 everywhere.

How tested

• cram_unmapped_sweep_returns_only_unplaced_records now also checks that the per-reference fetches plus the sweep return each record once for the multi-reference CRAM (before: r0, r1, r2, r3 each twice).
• New integration test test_parallel_cram_multi_reference_slice_counts_each_record_once: flagstat at --threads 1 and 4 must equal samtools 1.22.1's (before: 10 + 0 in total at -t 4).
• cargo test --release --locked --offline: 206 unit, 12 bin, 20 integration, 2 doc tests pass. cargo fmt --check passes. cargo clippy -- -D warnings reports the same three needless_range_loop errors as unmodified main with the local toolchain (clippy 0.1.90); with that lint allowed, --all-targets is clean.

Not changed, and why

• Records are still decoded and then dropped; filtering earlier, at the slice level, would need changes in noodles.
• BAM is unaffected: its per-reference path already checks the reference ID.

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