Sketchlib v2.1.4

Very minor update to remove the annoying mismatched versions warning

Also updated the CI to use CUDA 12.6

What's Changed

• Fix broken PopPUNK link & replace with valid site by @ctb in #95
• Remove the mismatched version warning by @johnlees in #97

New Contributors

• @ctb made their first contribution in #95

Full Changelog: v2.1.3...v2.1.4

Sketchlib v2.1.3

• Replace robin_hood hashmap (no longer maintained) with unordered_dense
• Add local mode for testing/customising compilation
• Fix efficiency of query sparse modes

What's Changed

• Improve efficiency of sparse queries by @johnlees in #94

Full Changelog: v2.1.2...v2.1.3

Sketchlib v2.1.2

• Fix a previously undetected segfault when multithreaded
• Hopefully(!) fix for new clang compilers

What's Changed

• Fix for adding random sequence correction for strand-specific k-mers by @nickjcroucher in #90
• Attempt to fix for clang 15 by @johnlees in #93

Full Changelog: v2.1.1...v2.1.2

Sketchlib v2.1.1

Small improvement to poor regressions, to fix a CI failure in PopPUNK

What's Changed

• Fix buildkite by @johnlees in #87
• More robust regression with zero distances by @johnlees in #88

Full Changelog: v2.1.0...v2.1.1

Sketchlib v2.1.0

• Remove armadillo from the code entirely in favour of Eigen
• Actually link BLAS (used in the regression), LAPACK not actually needed
• Use a new regression solver, see 'Normal equations' under https://eigen.tuxfamily.org/dox/group__LeastSquares.html
• Solve issues with bool in highfive code, now uint8_t explicitly used
• Use KMeansRex, as the kmeans in armadillo is now removed

nvcc now sees the eigen code and throws up a few warnings, but this doesn't seem to be causing as many problems as it used to

What's Changed

• BLAS linking; CI fix; better message for deprecated function by @johnlees in #84

Full Changelog: v2.0.1...v2.1.0

Sketchlib v2.0.1

Minor update which should not change/break the API, adds a few small new features. #82 simplifies and parallelises sparsification by a threshold (and removes kNN).

What's Changed

• Change web sketch output from uint64 to hex by @muppi1993 in #74
• Update README.md by @danrlu in #75
• Add reads attribute to databases by @johnlees in #77
• Lineage model fitting - sketchlib changes by @nickjcroucher in #82

New Contributors

• @muppi1993 made their first contribution in #74
• @danrlu made their first contribution in #75

Full Changelog: v2.0.0...v2.0.1

Sketchlib v2.0.0

This is a new major version due to overhaul of the CLI.

New features:

• CLI is now written with docopt, and should be more straightforward to use (#72).
• New self sparse query, which works with CUDA too (#67). Used in mandrake.

Bug fixes:

• Sparsification functions fixed and added to tests.

Other:

• Enable pip install and pushing to pypi (#70)
• Adding docker build and test on buildkite (#70)

Sketchlib 1.7.4

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 (#64)
• Better progress meter for read sketching (#64)
• Save whether the DB was calculated using the reverse complement strand (#65)

Bug fixes:

• Fix indices for reference vs query distance calculations, hit when reaching ~100k queries (#64)
• 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. (#64)

Other:

• Refactor the CUDA code a bit, putting classes into their own files. (#64)

Sketchlib 1.7.3

New features:

• Better parallel efficiency for distance calculation on a CPU (#62)

Bug fixes:

• Progress meter caused crash with small numbers of distances (#62)
• Smoother progress meter for distances (#62)
• Remove device reset which could cause problems with both GPU dists and a GPU graph in poppunk (#62)

Sketchlib 1.7.2

New features:

• Progress bars for main CPU functions #61
• Handle Ctrl-C in both CPU and GPU functions #38

Bug fixes:

• Deal with errors during sketching gracefully #61

Other:

• Change CMakeLists to work with gcc on OS X (to allow use of openmp)