cram: Bring reader and writer to htslib parity for CRAM 2.0–4.0#380
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Add full read/write support for CRAM versions 2.0, 2.1, 3.0, 3.1, and 4.0, reaching feature parity with htslib/samtools. This includes: Reader changes: - Legacy codec support (beta, gamma, Golomb, Huffman, subexp) for v2.x - CRAM 4.0 EOF detection, slice header encoding, and codec offsets - Async reader parity across all versions - Overflow protection for VLQ integer readers - Fix ref_seq_id encoding and codec argument signedness Writer changes: - Version-gated CRC32 checksums and qs_seq_orient encoding - fqzcomp HAVE_QMAP, HAVE_QTAB, MULTI_PARAM encoder features - Owned tag data and reference-free mode support - Name tokenizer tok_dup and fqzcomp DO_REV support API additions: - Reader::query_unmapped() and Reader::for_each_record() - IndexedReader delegation of the above methods Test infrastructure: - Programmatic in-memory test data creation (no on-disk test files) - Integration tests for round-trip, reader methods, query APIs, and writer options across all CRAM versions
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Summary
Full read/write support for CRAM versions 2.0, 2.1, 3.0, 3.1, and 4.0, reaching feature parity with htslib/samtools. See #374 for upstream context.
Reader
Writer
API additions
Reader::query_unmapped()andReader::for_each_record()IndexedReaderdelegation of the above methodsTest infrastructure
Files changed
97 files, +8285 / -1351 lines