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dUMI v2.0.0

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@github-actions github-actions released this 25 Jul 21:12
v2.0.0
92680cd

Added

  • Guarded streaming for compatible coordinate-sorted, single-end SAM/BAM
    input, with auto, on, and off control.
  • Runtime coordinate-order and leading-clipping validation.
  • Transactionally staged output for every advertised CLI route and direct
    Java entry point, plus an inner streaming-attempt boundary for safe legacy
    retry in auto mode.
  • Packed-key NgramBKTree routing with a general object-key fallback.
  • Differential data-structure tests, randomized reference comparisons, and
    regression coverage for deep trees, N-containing keys, threshold edges,
    parallel traversal, resource cleanup, and output transactions.
  • SAM/BAM/FASTQ command-line integration tests and a SAM/BAM compatibility and
    failure-safety matrix.
  • A public, reproducible benchmark harness with workload provenance,
    correctness gates, structured raw output, and paired baseline/candidate
    execution.
  • Java Flight Recorder allocation-profiling tools and aggregation guidance.
  • Cross-platform CI on supported Java runtimes, repository-hygiene checks, and
    byte-for-byte reproducible-build verification.
  • Checksum-locked runtime dependencies, a Java 11-targeted build, and an
    embedded build receipt identifying the exact production-source inputs.
  • A release pipeline that tests the tagged source, assembles a complete
    source-plus-binary archive, verifies the extracted archive, publishes
    checksums, an SPDX SBOM, and the build receipt, and creates a provenance
    attestation.
  • Contributor, security, citation, provenance, third-party licensing,
    architecture, optimization, limitations, and presentation-reference
    documentation.
  • Structured bug-report and feature-request forms, a pull-request template,
    and automated GitHub Actions dependency updates.

Changed

  • Compatible SAM/BAM runs default to guarded auto streaming.
  • Default underscore-delimited UMIs use a direct parser and encoder.
  • Average base quality is calculated lazily.
  • Sparse streaming groups bypass unnecessary general clustering setup.
  • Algorithm traversal and quality-based representative ties are deterministic;
    the any merge policy remains intentionally arbitrary.
  • Component and BK-tree traversal use explicit work queues rather than
    input-sized recursion.
  • Paired mate recovery supports indexed queries and sequential recovery for SAM
    or unindexed BAM input.
  • The launcher uses JVM heap defaults unless
    UMICOLLAPSE_JAVA_OPTS is supplied.
  • Streaming output is explicitly declared SO:unsorted.
  • Runtime dependencies are HTSJDK 3.0.5 and snappy-java 1.1.10.8.
  • Generated JARs are no longer tracked; builds and releases are produced from
    source with deterministic archive metadata.

Incorporated

  • The persistent paired-BAM reader change from canonical upstream PR
    #32, preserving
    its original commit authorship.
  • The n-gram object-allocation opportunity independently described in upstream
    PR #34.

Fixed

  • Resource cleanup around streaming fallback, paired readers, iterators, and
    writers.
  • Output preservation when forced streaming fails.
  • Custom UMI separators are interpreted literally.
  • Invalid explicit UMI lengths and UMIs shorter than the effective length are
    rejected rather than silently producing ambiguous encodings.
  • Invalid modes, options, ranges, strategy combinations, and same-file
    input/output requests fail before output processing, including path aliases
    and hard links that identify the same file.
  • Equality/hash contracts, generated-key metadata, and BitSet cloning
    preserve all encoded state.
  • Threshold arithmetic, packed-key boundaries, queue capacity, and deep-input
    traversal avoid overflow and stack-exhaustion failures.
  • Singleton inputs through extension entry points retain the requested merge
    behavior.
  • Cross-platform shell behavior for Bash 3 and Linux/macOS SHA-256 tooling.

Security and supply chain

  • GitHub Actions are pinned to immutable commit SHAs and run with restricted
    job permissions.
  • Locked Maven artifacts are audited against OSV on relevant pull requests, on
    demand, and on a weekly schedule.
  • Release inputs and dependencies are checksum-verified, generated artifacts
    are rejected from source control, and published assets are verified after
    upload.
  • Third-party notices and dependency license texts are included in the source
    tree and release archive.
Assets 6
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