dkoslicki CMash issues - Githubissues

dkoslicki / CMash

Fast and accurate set similarity estimation via containment min hash

BSD 3-Clause "New" or "Revised" License

42 stars 9 forks source link

issues

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Is CMash metric?

#32 jianshu93 opened 1 year ago
4
Add KMC as requirement

#31 dkoslicki opened 4 years ago
0
Ground truth computation is too slow for realistic data set sizes

#30 dkoslicki closed 4 years ago
1
For very large databases, creation of TST is slow and memory intensive

#29 dkoslicki opened 4 years ago
6
Gzipping all training files results in a nice reduction: add feature that allows scripts/modules to handle this

#28 dkoslicki opened 4 years ago
0
In MakeStreamingDNADatabase.py, don't require output directory to exist

#27 dkoslicki opened 4 years ago
0
Create script to demonstrate how to re-train CMash

#26 dkoslicki opened 4 years ago
0
Minor refactor of Query.py

#25 dkoslicki closed 4 years ago
1
Modularize StreamingQueryDNADatabase.py

#24 dkoslicki closed 4 years ago
3
In post-processing, find correct denominator

#23 dkoslicki opened 4 years ago
0
StreamingQueryDNA... may be case sensitive to sequences

#22 dkoslicki closed 4 years ago
1
Test k-mer frequency distribution idea

#21 dkoslicki opened 4 years ago
2
Multiple k-mer sizes confirmation and testing

#20 dkoslicki opened 4 years ago
2
Multiple k-mer sizes bug

#19 dkoslicki closed 4 years ago
2
Restructure repo so it's clear which approach is using the streaming, and which is using Bloom filters

#18 dkoslicki opened 4 years ago
0
Update PyPi release of CMash

#17 dkoslicki opened 4 years ago
0
Make a Conda/bioconda release of CMash

#16 dkoslicki opened 4 years ago
3
Improved classification time with KMC

#15 dkoslicki opened 4 years ago
16
Testing environment

#14 dkoslicki opened 4 years ago
9
Make python 3 compliant

#13 dkoslicki closed 4 years ago
0
Python3 hanging

#12 dkoslicki closed 4 years ago
2
Require pandas version>=0.21.1

#11 dkoslicki closed 5 years ago
0
Make sure jaccard isn't counting blanks/Inf as matches

#10 dkoslicki closed 4 years ago
1
k-merization makes no attempt to avoid Ns

#9 rsharris closed 4 years ago
3
Nondeterministic behavior of output queue

#8 dkoslicki closed 6 years ago
0
Deal with the duplicate small k-mers in the sketches

#7 dkoslicki closed 6 years ago
0
StreamingQuery isn't sharing the set

#6 dkoslicki closed 6 years ago
0
Parallelize the "collect the intersection counts"

#5 dkoslicki closed 6 years ago
1
Bloom filter for pre-filter of kmers

#4 dkoslicki closed 6 years ago
0
Installation woes -- TLSV1_ALERT_PROTOCOL_VERSION and pytest-runner

#3 rsharris closed 6 years ago
8
Figure out what to do with the reverse complements

#2 dkoslicki closed 4 years ago
2
Create LICENSE

#1 dkoslicki closed 7 years ago
0