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@ksahlin ksahlin released this 01 Apr 13:27
· 1360 commits to main since this release
v0.7
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Learn about vigilant mode.

Major update in the implemented parallelization. The new parallel implementation allows a much more efficient interplay with reading input -> aligning -> writing output. This results in much better CPU usage as the number of threads increases. For example, I observed an almost a 2x speedup (50-30% reduced runtime) across four larger datasets when using 16 cores (SIM and GIAB 150bp and 250bp reads, see README benchmarks).

For reference, previous naive parallelization ran in sequential order: 1. Read batch of reads with one thread 2. Align batch input in parallel with OpenMP 3. Write output with one thread. New parallelization performs 1-3 across threads with mutex on input and output. Such types of parallelization are commonly applied in other tools.

This release also includes:

  • Implemented automatic inference of read length, which removes the need of specifying -r (as reported in #19)
  • Some minor bugfixes. For example, this bug is fixed.

This release has identical or near-identical alignments to the previous version v0.6.1 (same accuracy and SV calling stats across tested datasets)

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