Update README and CHANGELOG for CRAM 3.1 write support (5.0.0)

Author: tfenne

CHANGELOG.md

@@ -10,6 +10,47 @@ early infrastructure for a plugin-based codec framework and resource bundles.
 
 ---
 
+## 5.0.0
+
+Adds **CRAM 3.1 write support** to htsjdk.  This is the culmination of the read-side codec work
+in 4.2.0 and the reader wiring in 4.3.0: htsjdk can now produce CRAM 3.1 files that are
+interoperable with samtools/htslib.
+
+### CRAM 3.1 Write Support
+
+- Enable CRAM 3.1 writing with all spec codecs: rANS Nx16, adaptive arithmetic Range coder, FQZComp, Name Tokenisation, and STRIPE
+- Add configurable compression profiles (FAST, NORMAL, BEST, ARCHIVE) with trial compression for automatic codec selection
+- Implement `TrialCompressor` to replace ad-hoc triple-compression for tags and align trial candidates with htslib
+- Add `GzipCodec` for direct Deflater/Inflater GZIP compression, wired into CRAM as a codec option
+- Strip NM/MD tags on CRAM encode and regenerate on decode, matching htslib behavior
+- Implement attached (same-slice) mate pair resolution
+- Align DataSeries content IDs with htslib for cross-implementation debugging
+- Remove unnecessary content digest tags from CRAM slice headers
+- Add `CramConverter` command-line tool for testing and benchmarking CRAM write profiles
+
+### Codec and Compression Optimizations
+
+- Refactor and optimize all rANS codecs: byte-array API, backwards-write encoding, and general simplifications
+- Optimize Name Tokeniser encoder: replace regex with hand-written parser; add per-type flags, STRIPE support, stream deduplication, and all-MATCH elimination
+- Optimize FQZComp, Range coder, and rANS encoder hot paths
+- Tune NORMAL profile codec assignments based on empirical compression testing
+
+### Performance
+
+- Replace `ByteArrayInputStream`/`ByteArrayOutputStream` with unsynchronized `CRAMByteReader`/`CRAMByteWriter` to eliminate synchronization overhead
+- Fuse read base restoration, CIGAR building, and NM/MD computation into a single pass during decode
+- Cache tag key metadata to eliminate per-record `String` allocation during CRAM decode
+- Pool `RANSNx16Decode` instances in the Name Tokeniser
+- Optimize BAM nibble-to-ASCII base decoding with a bulk lookup table
+
+### Testing and Infrastructure
+
+- Split CRAM 3.1 fidelity tests into per-profile classes for parallel execution
+- Reduce memory pressure in unit tests to eliminate OOM failures
+- Fix thread-safety bug in `VariantContextTestProvider` causing non-deterministic test counts
+
+---
+
 ## 4.3.0 (2025-05-09)
 
 Completes CRAM 3.1 read support by wiring the codec implementations (added in 4.2.0) into

README.md

@@ -11,6 +11,8 @@ manipulating HTS data.
 
 > **NOTE: _HTSJDK has only partial support for the latest Variant Call Format Specification.  VCFv4.3 can be read but not written, VCFv4.4 can be read in lenient mode only, and there is no support for BCFv2.2._**
 
+> **NOTE: _HTSJDK now supports both reading and writing CRAM 3.1 files.  CRAM 3.1 write support includes all codecs defined in the specification (rANS Nx16, adaptive arithmetic Range coder, FQZComp, Name Tokenisation, and STRIPE), configurable compression profiles (FAST, NORMAL, BEST, ARCHIVE), and trial compression for automatic codec selection.  Files produced by htsjdk are interoperable with samtools/htslib._**
+
 ### Documentation & Getting Help
 
 API documentation for all versions of HTSJDK since `1.128` are available through [javadoc.io](http://www.javadoc.io/doc/com.github.samtools/htsjdk).