Full CRAM 3.1 support & performance tuning of CRAM read/write#1763

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tfenne wants to merge 43 commits intodevfrom

Commits on Apr 11, 2026

Enable a naive CRAM 3.1 write profile.

cmnbroad
authored and
tfenne
committed
Changes based on instrumented trial runs.

cmnbroad
authored and
tfenne
committed
CRAM 3.1 write tests and code cleanup.

cmnbroad
authored and
tfenne
committed
Temp fix for preSorted=false default.

cmnbroad
authored and
tfenne
committed
Add CRAM 3.1 codec implementations: STRIPE, FQZComp encoder, and Range helpers.
tfenne
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Add CRAM compression profiles with trial compression for codec selection.
tfenne
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Add CramConverter command-line tool for testing CRAM write profiles.
tfenne
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Strip NM/MD on CRAM encode, regenerate on decode, and implement attached mate pairs.
tfenne
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Optimize NORMAL profile codec assignments based on empirical compression testing.
tfenne
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Align DataSeries content IDs with htslib for cross-implementation debugging.
tfenne
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Split CRAM31 fidelity tests into per-profile classes for parallel execution.
tfenne
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Fix TrialCompressor method tracking and align SMALL/ARCHIVE trial candidates with htslib.
tfenne
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Optimize name tokeniser compression with per-type flags, STRIPE, stream dedup, and all-MATCH elimination.
tfenne
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Add GzipCodec for direct Deflater/Inflater GZIP compression and wire into CRAM.
tfenne
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Replace ad-hoc triple-compression for tags with TrialCompressor.
tfenne
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Refactor and optimize all rANS codecs: byte[] API, backwards-write, simplifications.
tfenne
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Reduce memory pressure in unit tests to eliminate OOM failures.
tfenne
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Tune codec assignments and tag trial compression for better compression.
tfenne
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Optimize FQZComp/Range coder and rANS encoder hot paths.
tfenne
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Optimize name tokeniser encoder: replace regex with hand-written parsing.
tfenne
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Remove unnecessary content digest tags from CRAM slice headers.
tfenne
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Pool RANSNx16Decode instance in name tokeniser and make CramConverter output optional.
tfenne
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Replace ByteArrayInputStream/OutputStream with unsynchronized CRAMByteReader/Writer.
tfenne
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Fix thread-safety bug in VariantContextTestProvider causing non-deterministic test counts.
tfenne
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Fuse read base restoration, CIGAR building, and NM/MD computation into single pass.
tfenne
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Cache tag key metadata to eliminate per-record String allocation during CRAM decode.
tfenne
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Update README and CHANGELOG for CRAM 3.1 write support (5.0.0)
tfenne
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Fix LibdeflateDeflater/Inflater compatibility with ByteBuffer API.
tfenne
committed

Commits on Apr 12, 2026