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andi v0.8
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@kloetzl kloetzl released this 19 Dec 16:55
· 492 commits to master since this release
v0.8
4482df1

This is the holiday release of andi. It is faster and uses less memory than previous versions, so the numbers in the paper are outdated. The runtime on the Meala 3085 data set is now 6 hours and 21 minutes with just 10.9 GB of memory. That is a 12% speed up and only half the memory. For the smaller datasets the improvements are less noticeable.

Please load the attached andi-0.8.tar.gz and follow the instructions in the Readme.md for building.

The changes include

  • Introduction of a novel first variant character (FVC) array, resulting in improved performance
  • Fixed bugs on singleton intervals
  • Fixed a bug resulting in nan or incomplete comparisons for very closely related sequences.
  • Reduced memory usage by freeing the reverse complement of a sequence when it is no longer needed.
  • Various micro optimizations.
Assets 3