Published July 22, 2021 | Version v1.7.4
Software Open

johnlees/pp-sketchlib: Sketchlib 1.7.4

Authors/Creators

  • 1. Imperial College London

Description

New features:

  • Sketching kernel overhaul: should be faster, and supports read datasets larger than the device memory size (#63 #64)
  • Increase the size of the countmin table on GPUs to 2^30 columns, takes up about 30% of a 3090's memory
  • Better progress meter for read sketching
  • Save whether the DB was calculated using the reverse complement strand

Bug fixes:

  • Fix indices for reference vs query distance calculations, hit when reaching ~100k queries
  • If sketching craps out early, save the successful sketches up until that point to the HDF5 DB without corrupting it, so it can be joined later.

Other:

  • Refactor the CUDA code a bit, putting classes into their own files.

Files

johnlees/pp-sketchlib-v1.7.4.zip

Files (25.8 MB)

Name Size Download all
md5:c1b0c9e87567c3a055bfcba209d891fc
25.8 MB Preview Download

Additional details

Related works