Ecosyste.ms: Issues

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GitHub / dkoslicki/CMash issues and pull requests

#32 - Is CMash metric?

Issue - State: open - Opened by jianshu93 over 1 year ago - 4 comments

#31 - Add KMC as requirement

Issue - State: open - Opened by dkoslicki over 4 years ago

#30 - Ground truth computation is too slow for realistic data set sizes

Issue - State: closed - Opened by dkoslicki over 4 years ago - 1 comment
Labels: priority

#29 - For very large databases, creation of TST is slow and memory intensive

Issue - State: open - Opened by dkoslicki over 4 years ago - 6 comments
Labels: enhancement, priority

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

Issue - State: open - Opened by dkoslicki over 4 years ago
Labels: enhancement, good first issue

#27 - In MakeStreamingDNADatabase.py, don't require output directory to exist

Issue - State: open - Opened by dkoslicki over 4 years ago
Labels: good first issue

#26 - Create script to demonstrate how to re-train CMash

Issue - State: open - Opened by dkoslicki over 4 years ago

#25 - Minor refactor of Query.py

Issue - State: closed - Opened by dkoslicki over 4 years ago - 1 comment

#24 - Modularize StreamingQueryDNADatabase.py

Issue - State: closed - Opened by dkoslicki over 4 years ago - 3 comments

#23 - In post-processing, find correct denominator

Issue - State: open - Opened by dkoslicki over 4 years ago

#22 - StreamingQueryDNA... may be case sensitive to sequences

Issue - State: closed - Opened by dkoslicki over 4 years ago - 1 comment

#21 - Test k-mer frequency distribution idea

Issue - State: open - Opened by dkoslicki almost 5 years ago - 2 comments

#20 - Multiple k-mer sizes confirmation and testing

Issue - State: open - Opened by dkoslicki almost 5 years ago - 2 comments
Labels: priority

#19 - Multiple k-mer sizes bug

Issue - State: closed - Opened by dkoslicki almost 5 years ago - 2 comments

#17 - Update PyPi release of CMash

Issue - State: open - Opened by dkoslicki almost 5 years ago

#16 - Make a Conda/bioconda release of CMash

Issue - State: open - Opened by dkoslicki almost 5 years ago - 3 comments
Labels: good first issue

#15 - Improved classification time with KMC

Issue - State: open - Opened by dkoslicki almost 5 years ago - 16 comments
Labels: enhancement, good first issue

#14 - Testing environment

Issue - State: open - Opened by dkoslicki almost 5 years ago - 9 comments
Labels: good first issue

#13 - Make python 3 compliant

Issue - State: closed - Opened by dkoslicki almost 5 years ago

#12 - Python3 hanging

Issue - State: closed - Opened by dkoslicki almost 5 years ago - 2 comments

#11 - Require pandas version>=0.21.1

Issue - State: closed - Opened by dkoslicki about 5 years ago

#10 - Make sure jaccard isn't counting blanks/Inf as matches

Issue - State: closed - Opened by dkoslicki almost 6 years ago - 1 comment
Labels: bug

#9 - k-merization makes no attempt to avoid Ns

Issue - State: closed - Opened by rsharris over 6 years ago - 3 comments

#8 - Nondeterministic behavior of output queue

Issue - State: closed - Opened by dkoslicki over 6 years ago

#7 - Deal with the duplicate small k-mers in the sketches

Issue - State: closed - Opened by dkoslicki over 6 years ago

#6 - StreamingQuery isn't sharing the set

Issue - State: closed - Opened by dkoslicki over 6 years ago
Labels: bug

#5 - Parallelize the "collect the intersection counts"

Issue - State: closed - Opened by dkoslicki over 6 years ago - 1 comment
Labels: enhancement

#4 - Bloom filter for pre-filter of kmers

Issue - State: closed - Opened by dkoslicki over 6 years ago
Labels: enhancement, priority

#3 - Installation woes -- TLSV1_ALERT_PROTOCOL_VERSION and pytest-runner

Issue - State: closed - Opened by rsharris over 6 years ago - 8 comments

#2 - Figure out what to do with the reverse complements

Issue - State: closed - Opened by dkoslicki over 6 years ago - 2 comments

#1 - Create LICENSE

Pull Request - State: closed - Opened by dkoslicki about 7 years ago