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HiPhase v1.1.0
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@holtjma holtjma released this 04 Dec 19:15
· 21 commits to main since this release
v1.1.0
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Learn about vigilant mode.

Changes

  • Updated the way unphaseable variants are placed into artificial phase blocks. Instead of unphased singletons, these are now grouped into larger unphased blocks. Phased variants are unaffected by this change.
    • This has a major impact on I/O churning, especially in centromeric and telomeric regions. Internal tests show up to 60% reduction in wall clock time with 16 threads accompanied by up to 30% reduction in CPU time depending on the phasing mode.
    • There are now fewer total phase blocks reported due to the singleton collapse. This primarily impacts the statistic tracking optional outputs of HiPhase.

Fixed

  • Fixed a related issue where unphased singleton blocks were falsely tagged with TR_OVERLAP
  • Fixed an issue where the default --io-threads frequently caused issues on long-running jobs. This now defaults to min(--threads, 4), but can still be specified with --io-threads.
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