bacpop/pp-sketchlib

Issues

• Clang 15 compilation issues on macOS

  #92 opened 9 months ago by jakirkham
  6

• Idea for faster distances

  #91 opened a year ago by johnlees
  0

• Add support for proteomes

  #89 opened 2 years ago by johnlees
  0

• Try replacing `ldlt` with `llt` in solver, link LAPACK

  #85 opened 2 years ago by johnlees
  1

• GPU out of memory - countmin table size

  #86 opened 2 years ago by yuragal
  17

• Dealing with h5 files

  #81 opened 2 years ago by andreaniml
  6

• Use nthashv2 for codon-phased seeds

  #79 opened 2 years ago by johnlees
  0

• Compatibility issues with hdf5?

  #78 opened 2 years ago by dpryan79
  4

• conda build for OS X doesn't link openmp

  #76 opened 2 years ago by johnlees
  1

• HDF5 file needs to be split into multiple groups

  #71 opened 2 years ago by johnlees
  1

• System OpenMP used for linking when building, conda OpenMP used when running

  #42 opened 2 years ago by johnlees
  2

• Allow sketching & Jaccard distance at single k-mer length

  #58 opened 2 years ago by johnlees
  1

• Keep hash of seq in DB

  #73 opened 2 years ago by johnlees
  0

• sketch_size is divided twice (?)

  #69 opened 2 years ago by SteMIDIfactory
  3

• Use the proper dust RNG library

  #68 opened 3 years ago by johnlees
  0

• Add strand attribute to DBs

  #65 opened 3 years ago by johnlees
  1

• Allow partial processing of read datasets

  #63 opened 3 years ago by johnlees
  1

• Handle keyboard interrupt from python

  #38 opened 3 years ago by johnlees
  1

• Error when querying database without all samples in RandomMC

  #55 opened 4 years ago by johnlees
  0

• ZFP compression of distance matrix

  #53 opened 4 years ago by johnlees
  2

• Memory map/manage large arrays through disk storage

  #54 opened 4 years ago by johnlees
  0

• Make distance calculation read only from HDF5

  #51 opened 4 years ago by johnlees
  0

• Alternative sketch IO formats

  #37 opened 4 years ago by johnlees
  2

• Remove network boundary and iterate functions

  #49 opened 4 years ago by johnlees
  0

• Network refinement helper

  #46 opened 4 years ago by johnlees
  1

• Add AVX-512 instruction support

  #13 opened 4 years ago by johnlees
  4

• Next conda release should use CMake

  #39 opened 4 years ago by johnlees
  0

• Add ability to load sketches into memory using python API

  #15 opened 5 years ago by johnlees
  1

• Better implementation of spaced seeds

  #29 opened 4 years ago by johnlees
  0

• GPU sketching

  #25 opened 4 years ago by johnlees
  1

• Allow construction of DB without calculating random match chance

  #28 opened 4 years ago by johnlees
  1

• Asynchronous GPU/CPU use in sketching

  #33 opened 4 years ago by johnlees
  1

• Allow Ns in GPU read sketching

  #34 opened 4 years ago by johnlees
  0

• Replace C++11 threads with OpenMP

  #30 opened 4 years ago by johnlees
  0

• Problem closing file

  #16 opened 4 years ago by nickjcroucher
  3

• Better random match chances

  #26 opened 4 years ago by johnlees
  0

• Break up ref v ref querying when GPU memory exceeded

  #20 opened 4 years ago by johnlees
  0

• Add matrix manipulation functions

  #19 opened 4 years ago by johnlees
  0

• Error with GPU distances

  #18 opened 4 years ago by johnlees
  3

• installing with conda

  #17 opened 4 years ago by flass
  19

• Improve k-mer filter

  #11 opened 5 years ago by johnlees
  3

• Installation problem on Linux

  #12 opened 5 years ago by nickjcroucher
  15

• Ensure when adding or merging, no duplicate names exist

  #10 opened 5 years ago by johnlees
  0

• Profile code

  #8 opened 5 years ago by johnlees
  11

• Support read input

  #4 opened 5 years ago by johnlees
  2

• Allow multiple sequence files per input sample

  #5 opened 5 years ago by johnlees
  0

• Make new python file in PopPUNK to interface with library

  #7 opened 5 years ago by johnlees
  1

• Test results on Listeria example dataset

  #9 opened 5 years ago by johnlees
  0

• Add python interface to Jaccard distances

  #2 opened 5 years ago by johnlees
  0

• Create python interface with pybind11

  #3 opened 5 years ago by johnlees
  0