Issues
- 5
Purpose of max kmer frequency?
#142 opened by peterk87 - 4
Output list of tiles that didn't match
#59 opened by dankein - 0
- 0
- 0
Feature Add: Toggle to run all schemes on a sample and report best matching scheme
#125 opened by jrober84 - 0
- 0
- 0
- 2
Update needed for S. Typhi scheme
#128 opened by glabbe - 2
SNV subtyping scheme creation tool
#43 opened by gcttong - 3
- 1
Raise MAX_KMER_FREQUENCY Value to 10,000
#101 opened by glabbe - 11
Output "NA" as subtype for samples that fail QC with no subtype result or no targets found
#112 opened by glabbe - 4
metadata file type
#108 opened by dankein - 4
Change tb_speciation to tb_lineage?
#107 opened by dankein - 1
Update New Release to Pypi
#95 opened by DarianHole - 0
Skipping a deployment with the pypi provider because this repo's name does not match one specified in .travis.yml's deploy.on.repo: phac-nml/bio_hansel
#104 opened by peterk87 - 3
- 1
Semicolons in version numbers for some schemes
#99 opened by peterk87 - 1
QC module not failing samples where positive and negative kmers are detected for the same genome position
#98 opened by glabbe - 0
- 8
Degenerate "probe" sequence expansion
#60 opened by peterk87 - 3
- 2
- 1
Link to docs in readme
#50 opened by peterk87 - 1
Re-order the match results to put the positive tiles matches at the top of the list
#72 opened by glabbe - 1
Add sample input grouping based on the regex `_(R1|R2)` to support Illumina instrument output
#38 opened by peterk87 - 1
Bionumerics CSV output option
#66 opened by peterk87 - 0
--min-kmer-freq is no longer adjustable
#61 opened by sond468 - 1
Command-line arg variable name and SubtypingParams instance variable name synchronization
#63 opened by peterk87 - 0
Empty files when no targets are found
#49 opened by peterk87 - 2
Shorten QC messages - remove repeated terms
#46 opened by glabbe - 1
tag v2.0.0 release
#44 opened by corburn - 0
Cannot parse gzipped seq files on Mac OSX since zcat doesn't work the same as under Linux
#39 opened by peterk87 - 1
- 1
Remove NCBI BLAST+ and Jellyfish dependencies
#29 opened by peterk87 - 4
Failing on custom TB dataset
#35 opened by Takadonet - 2
New Release Needed
#33 opened by mgopez - 1
Unconfident QC Check not behaving as expected
#27 opened by mgopez - 1
Error in QC join function
#25 opened by mgopez - 4
- 1
New Release
#24 opened by mgopez - 1
Raise MAX_KMER Value to 1000
#18 opened by mgopez - 1
Exception when running QC functions against FASTA `KeyError: 'is_kmer_freq_okay'`
#21 opened by peterk87 - 0
new technician output file format
#13 opened by Takadonet - 0
Quality assessment module
#14 opened by Takadonet - 1
Add downsampling to workflow
#16 opened by Takadonet - 0
Update Enteritidis scheme to v0.7.0
#11 opened by peterk87 - 3
Fix inconsistent subtype function
#10 opened by peterk87 - 7