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Implementation of CRAM 3.1 codecs.#1714

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cmnbroad wants to merge 27 commits intomastersamtools/htsjdk:masterfrom cn_cram_3_1_codecssamtools/htsjdk:cn_cram_3_1_codecsCopy head branch name to clipboard

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Commits

Commits on Dec 18, 2024

• Implementation of CRAM 3.1 codecs.

  

  yash-puligundla

  authored and

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• Many FQZComp fixes, with roundtrip tests working.

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  dd9b17e

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• Name tokenization codec fixes.

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• Interop test data from htslib.

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• Remove unnecessary mac files.

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• Use shared rans decoder in interop tests.

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• Update useArith type in name tokenizer, remove unecessary object creation in tests.

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• Remove sketchy exception suppression, make test encoding params type-safe, precompile the name Tok regex, eliminate unnecessary code.

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• Code cleanup.

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• Store token stream in arrays instead of lists.

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• More naming, removal of unnecessary code, switch sanitization.

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• Temp update.

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• Precompile regular expression patterns, optimize some string operations, fix the read name separator.

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• Checkpoint 1.

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• Checkpoint 2.

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• Repair haphazard stream management.

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• Consolidate and optimize, remove unecessary code.

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• Fix spotbugs issue.

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Commits on Jan 6, 2025

• Remove unnecessary code.

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  22e0dfa

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• Fix sketchy byte conversion to use UTF-8 charset for names.

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• Remove obsolete comment.

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• Upgrade to samtools 1.21.

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  a71f9a9

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• Remove redundant/duplicate tests.

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Commits on Jan 7, 2025

• Eliminate intermediate String representation for decoded names.

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• Standardize input/output read name buffer separator.

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  91c1cce

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• Update name separator handling.

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  2b4ffd8

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• Comment update.

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