dkoslicki/CMash

Issues

• Is CMash metric?

  #32 opened a year ago
  4

• Add KMC as requirement

  #31 opened 4 years ago
  0

• Ground truth computation is too slow for realistic data set sizes

  #30 opened 4 years ago
  1

• For very large databases, creation of TST is slow and memory intensive

  #29 opened 4 years ago
  6

• Gzipping all training files results in a nice reduction: add feature that allows scripts/modules to handle this

  #28 opened 4 years ago
  0

• In MakeStreamingDNADatabase.py, don't require output directory to exist

  #27 opened 4 years ago
  0

• Create script to demonstrate how to re-train CMash

  #26 opened 4 years ago
  0

• Minor refactor of Query.py

  #25 opened 4 years ago
  1

• Modularize StreamingQueryDNADatabase.py

  #24 opened 4 years ago
  3

• In post-processing, find correct denominator

  #23 opened 4 years ago
  0

• StreamingQueryDNA... may be case sensitive to sequences

  #22 opened 4 years ago
  1

• Test k-mer frequency distribution idea

  #21 opened 4 years ago
  2

• Multiple k-mer sizes confirmation and testing

  #20 opened 4 years ago
  2

• Multiple k-mer sizes bug

  #19 opened 4 years ago
  2

• Restructure repo so it's clear which approach is using the streaming, and which is using Bloom filters

  #18 opened 4 years ago
  0

• Update PyPi release of CMash

  #17 opened 4 years ago
  0

• Make a Conda/bioconda release of CMash

  #16 opened 4 years ago
  3

• Improved classification time with KMC

  #15 opened 4 years ago
  16

• Testing environment

  #14 opened 4 years ago
  9

• Make python 3 compliant

  #13 opened 5 years ago
  0

• Python3 hanging

  #12 opened 5 years ago
  2

• Require pandas version>=0.21.1

  #11 opened 5 years ago
  0

• Make sure jaccard isn't counting blanks/Inf as matches

  #10 opened 5 years ago
  1

• k-merization makes no attempt to avoid Ns

  #9 opened 5 years ago
  3

• Nondeterministic behavior of output queue

  #8 opened 6 years ago
  0

• Deal with the duplicate small k-mers in the sketches

  #7 opened 6 years ago
  0

• StreamingQuery isn't sharing the set

  #6 opened 6 years ago
  0

• Parallelize the "collect the intersection counts"

  #5 opened 6 years ago
  1

• Bloom filter for pre-filter of kmers

  #4 opened 6 years ago
  0

• Installation woes -- TLSV1_ALERT_PROTOCOL_VERSION and pytest-runner

  #3 opened 6 years ago
  8

• Figure out what to do with the reverse complements

  #2 opened 4 years ago
  2