70 improve zstd decompression times

[noamteyssier]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @noamteyssier, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on significantly improving the Zstd decompression performance within the binseq library. The changes involve migrating to a more efficient Zstd API, implementing reusable decompression contexts, and optimizing the block processing workflow. These enhancements aim to reduce memory overhead and accelerate the reading of compressed sequencing data, ultimately leading to faster application execution.

Highlights

• Zstd Decompression Optimization: Switched the Zstd decompression implementation from zstd::Decoder to the lower-level zstd::zstd_safe API to gain more control over the decompression process.
• Reusable Decompression Context: Introduced a reusable Zstd decompression context (DCtx) within the RecordBlock struct. This avoids repeated allocation and initialization of decompression contexts, leading to performance improvements.
• Efficient Block Processing: Refactored the ingest_compressed_bytes method to decompress entire blocks into a pre-allocated reusable buffer (rbuf) using the DCtx. The parsing of individual records is then performed on this decompressed buffer, reducing memory allocations and improving overall speed.
• Code Refactoring: Extracted the common record parsing logic into a new private helper function ingest_bytes, which is now called by both the direct byte ingestion and the compressed byte ingestion after decompression.

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[gemini-code-assist]

Code Review

This pull request significantly improves zstd decompression performance by reusing the decompression context and processing blocks in a single operation, which is a great enhancement. The refactoring of ingest_bytes into a standalone function also improves code clarity and reuse. However, I've identified a critical bug in the implementation of ingest_compressed_bytes that will prevent decompression from working as intended, along with a minor documentation issue. Addressing these points will make this a solid contribution.