medvir/VirMet

Issues

• Build database virus

  #29 opened 7 years ago by Castell34
  7

• AssertionError

  #52 opened 4 years ago by Vikash84
  0

• `virmet covplot` for viruses with a segmented genome

  #46 opened 6 years ago by sschmutz
  1

• docker scripts point to wrong ftp addresses for fetching genomes

  #41 opened 4 years ago by msegurawang
  0

• virmet wolfpack --run doesn't work if run_name starts with a 2

  #50 opened 4 years ago by sschmutz
  1

• virmet covplot not working because of missing ggplot package

  #49 opened 4 years ago by mihuber
  1

• read_table is deprecated, use read_csv instead

  #47 opened 5 years ago by sschmutz
  1

• virmet tidytable does not finish if one sample doesn't contain any viral reads

  #39 opened 5 years ago by sschmutz
  0

• Read counts in covplot is overestimated

  #37 opened 7 years ago by ozagordi
  0

• if ssciname in unique.tsv is N/A, no entry is written in orgs_list.tsv

  #42 opened 6 years ago by sschmutz
  0

• Read counts in orgs_list.tsv is underestimated for some species.

  #44 opened 6 years ago by MaryamZaheri
  1

• virmet readthedocs website not displayed properly

  #43 opened 6 years ago by sschmutz
  0

• Quality filtering of NanoPore reads

  #25 opened 7 years ago by mihuber
  3

• Command to update fungal db, check also bacterial update

  #12 opened 9 years ago by ozagordi
  0

• More aggressive clean up

  #13 opened 9 years ago by ozagordi
  0

• Write `covplot` documentation

  #14 opened 8 years ago by ozagordi
  0

• Adapt to phase out of genbank identifiers

  #16 opened 8 years ago by ozagordi
  0

• FutureDeprecation warning in `covplot.py`

  #17 opened 8 years ago by ozagordi
  0

• TidyData Table

  #18 opened 8 years ago by mihuber
  0

• Bug in tidytable

  #20 opened 7 years ago by mihuber
  0

• FileNotFoundError when running single files

  #21 opened 7 years ago by mihuber
  0

• Error when no viral reads are found: AttributeError: 'Series'

  #22 opened 7 years ago by ozagordi
  1

• wolfpack

  #31 opened 7 years ago by LCarioti
  12

• Download taxonomy files

  #36 opened 7 years ago by ozagordi
  0

• Gini index

  #38 opened 6 years ago by mihuber
  0

• Logging improvements

  #6 opened 9 years ago by ozagordi
  0

• Reporting

  #8 opened 9 years ago by mihuber
  1

• Output

  #4 opened 9 years ago by mihuber
  2

• Input

  #5 opened 9 years ago by mihuber
  0

• Locking strategy

  #10 opened 9 years ago by ozagordi
  0

• Matching contaminant

  #11 opened 9 years ago by ozagordi
  0

• Fetching databases in parallel

  #9 opened 9 years ago by ozagordi
  1

• When picked_seqs are present, they must be added to viral_gi_taxid.dmp

  #3 opened 9 years ago by ozagordi
  1

• Run `makeblastdb` at the end of `fetch_viral_genomes.py`

  #2 opened 9 years ago by ozagordi
  1

• Document hot run capabilities

  #40 opened 6 years ago by ozagordi
  0

• Write better output for `update`

  #19 opened 7 years ago by ozagordi
  0

• Version of VirMet and virus reference database

  #26 opened 7 years ago by mihuber
  4

• depth.txt is overwritten if you run covplot more than once

  #28 opened 7 years ago by sschmutz
  1

• add measured variable of coverage and species information

  #32 opened 7 years ago by sschmutz
  0

• *coverage.pdf of large genomes not displayed properly

  #33 opened 7 years ago by sschmutz
  0

• Update search query to include all viral genomes

  #34 opened 7 years ago by ozagordi
  0

• ./ or ../ as --outdir argument in tidytable.py leads to an error

  #30 opened 7 years ago by sschmutz
  1

• Re-analysis of samples

  #24 opened 7 years ago by mihuber
  2

• Virus reads used for alignment covplot

  #27 opened 7 years ago by mihuber
  1

• Adapt to phasing out of GI numbers by NCBI.

  #15 opened 8 years ago by ozagordi
  0

• Coverage plot

  #7 opened 9 years ago by ozagordi
  0

• Inconsistency of viral reads count.

  #1 opened 10 years ago by ozagordi
  0