KoslickiLab/YACHT

Issues

• Yacht usage article

  #113 opened a year ago by mfl15
  3

• Training doesn't like sig files

  #67 opened a year ago by dkoslicki
  8

• Set default parameters to be what was best on the CAMI data

  #118 opened a year ago by dkoslicki
  0

• Cover yacht convert with tests

  #116 opened a year ago by mfl15
  0

• Error in yacht convert

  #114 opened a year ago by OliverBryan
  6

• Performance testing

  #110 opened a year ago by mfl15
  0

• Create wiki documentation - Developer docs

  #109 opened a year ago by mfl15
  0

• Optimize code speed

  #108 opened a year ago by mfl15
  0

• Auto-handling of gzip, tar.gz, zip, xz compressed FASTA/FASTQ files

  #107 opened a year ago by mfl15
  0

• Provide use-case examples

  #6 opened 2 years ago by dkoslicki
  0

• Make a test of using pre-trained data

  #87 opened a year ago by dkoslicki
  0

• Error working with GTDB database

  #103 opened a year ago by OliverBryan
  2

• Add test to look for `abspath` error

  #44 opened a year ago by dkoslicki
  0

• Training step throws an error with empty/small sketches, should report reason and make a suggestion to fix

  #12 opened a year ago by Electrocyte
  2

• When downloading from Zenodo, the config files need updated

  #85 opened a year ago by dkoslicki
  2

• Yacht training takes ~90min for GTDB r214 representative

  #91 opened a year ago by ShaopengLiu1
  2

• Investigate C/Rust implementation

  #8 opened a year ago by dkoslicki
  1

• bug: `os.exit`

  #86 opened a year ago by dkoslicki
  1

• Create a release for YACHT

  #1 opened a year ago by gregorysprenger
  2

• Expand readme, clarify inputs, etc. (Enhancement)

  #2 opened a year ago by gregorysprenger
  2

• Add a warning to users that training step on the entire GTDB will take significant amount of time

  #49 opened a year ago by kodh49
  3

• Setup file still says there was a problem

  #47 opened a year ago by dkoslicki
  1

• Check if a sig.zip file has a manifest in it

  #39 opened a year ago by dkoslicki
  0

• Add demo workflow to the tests

  #40 opened a year ago by dkoslicki
  0

• add --force flag for overwriting existing training data

  #37 opened a year ago by dkoslicki
  0

• Remove extraneous --dirname and --filename

  #38 opened a year ago by dkoslicki
  0

• Make test and runtime check for only single sketch in .zip file for the sample

  #34 opened a year ago by dkoslicki
  0

• CAMI output format issue

  #32 opened a year ago by dkoslicki
  2

• Uncaught runtime error

  #36 opened a year ago by dkoslicki
  2

• Fix tests for new training method

  #35 opened a year ago by dkoslicki
  0

• install issue

  #30 opened a year ago by dkoslicki
  8

• Optimize the code to reduce RAM usage

  #21 opened a year ago by chunyuma
  1

• Relative import error in conversion script

  #31 opened a year ago by dkoslicki
  0

• standardize output format

  #7 opened a year ago by dkoslicki
  2

• Output format needs attention

  #13 opened a year ago by dkoslicki
  3

• Need test suites

  #5 opened a year ago by dkoslicki
  0

• run_YACHT.py: error: the following arguments are required: --database_prefix, --outdir

  #19 opened 2 years ago by mfl15
  0

• Dependencies, requirements.txt, and conda (Enhancement)

  #3 opened 2 years ago by gregorysprenger
  1

• Uncaught error

  #15 opened 2 years ago by dkoslicki
  2

• tqdm not in requirements

  #14 opened 2 years ago by dkoslicki
  1

• Refactor to make workflow clearer

  #4 opened 2 years ago by dkoslicki
  0

• refactor recover_abundance.py

  #9 opened 2 years ago by dkoslicki
  0

• Move to dataframes instead of tons of numpy array

  #11 opened 2 years ago by dkoslicki
  0

• Use exact instead of approximate Binomail CDF calculation

  #10 opened 2 years ago by dkoslicki
  0