Sketchlib 1.5.1

Important bugfix (see bacpop/PopPUNK#95):

• Inputs to the CPU query API were being sorted by name, returning distances not in the expected order. This will have worked with poppunk_sketch but not through other software such as PopPUNK, unless the input was alphabetical.

Sketchlib v1.5.0

New features:

• Allow turning off random match computation (#28), which is useful for querying.
• Replace threads with OpenMP (#31). Much more efficient CPU parallelisation of distances.
• Add GPU/CPU hybrid sketching algorithm for read data (#32).
• Add codon phased seeds --codon-phased (#35). This replaces randomly spaced seeds.

Bug fixes:

• Update to work with HighFive v2.2.2
• Check for zero Jaccard distances (#36)

Random match correction

New features:

• Add parallelised sparse and dense matrix operations (#21, #23)
• Used spaced seeds in hash function; store sketching version in HDF5 file (#22)
• Chunk up distance calculation on the GPU, so any size is supported (#24)
• Calculate random match chances via Monte Carlo simulation (#27)

Added CI testing:

• Add new tests for matrix functions
• Add test for distances compared to reference values

Test to be manually run:

• Compare GPU and CPU distances

K-mer length enhancements

Adds the following features:

• Extract Jaccard distances
• Calculate and save genome length using minimum hash
• Calculate and save base composition
• Adjust comparisons for base composition, and expected random matches
• Spaced seeds for short k-mer lengths

Bug fixes:

• Error when calculating distances on a GPU (#18)

GPU accelerated distances

New features:

• Distance calculations on CUDA compatible GPUs.
• Use armadillo linear solver rather than dlib for regressions (on CPU).

Added some benchmarks to the readme

Improved speed and memory

New features:

• Implement countmin correctly and pick sensible default parameters for sketching read datasets (#11)
• More reliable and faster code for optimiser used in linear regression
• Add testing and CI

Bug fixes:

• Made CMakeLists.txt and Makefile more general (removed specific paths)

Patched release

Small fixes:

• #14: Use the mkl_rt library to link, which works better with conda (see https://groups.google.com/forum/#!msg/kaldi-help/m3nyQke0HS0/4fj8gkSWAgAJ, https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/748309, ContinuumIO/anaconda-issues#720)
• #14: As the sequential library cannot be specified, export this as an environment variable in the api.cpp functions which handle their own threading.
• Correct version of gcc used to compile

Initial release

Features tested and working on OS X and Linux. Install looks ok, locally