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oxfordmmm
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gnomonicus
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
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bump: gumpy 1.3.3
#75
JeremyWesthead
closed
2 days ago
0
bump: use gumpy 1.3.2
#74
JeremyWesthead
closed
1 week ago
0
fix: make sure duplicate rows can't make it through
#73
JeremyWesthead
closed
1 week ago
0
bump: vcf_subset 1.1.2
#72
JeremyWesthead
closed
2 weeks ago
0
bump: version++
#71
JeremyWesthead
closed
2 weeks ago
0
bump: gumpy 1.3.1
#70
JeremyWesthead
closed
2 weeks ago
0
fix: ensure all minos positions from merge-vcfs
#69
JeremyWesthead
closed
2 weeks ago
0
Feat/gvcf support
#68
JeremyWesthead
closed
2 weeks ago
0
bump: version to 2.5.7
#67
JeremyWesthead
closed
3 weeks ago
0
Fix/dont fasta adjudicate deletions
#66
JeremyWesthead
closed
3 weeks ago
0
fix: bump version
#65
mcolpus
closed
1 month ago
0
fix: order variants better
#64
mcolpus
closed
1 month ago
0
fix: ensure docker build runs
#63
JeremyWesthead
closed
1 month ago
0
fix: bump version for release
#62
JeremyWesthead
closed
2 months ago
0
fix: ensure that fasta adjudication happens, even in cases of 0 mutat…
#61
JeremyWesthead
closed
2 months ago
2
Fix/sort json
#60
mcolpus
closed
2 months ago
0
fix: bump piezo to ensure epistasis rules + pass resistance subset ar…
#59
JeremyWesthead
closed
3 months ago
0
fix: bump gumpy version
#58
JeremyWesthead
closed
3 months ago
0
fix: bump piezo version
#57
JeremyWesthead
closed
3 months ago
0
Feat/epistasis support
#56
JeremyWesthead
closed
3 months ago
0
fix(update-table): ensure append on outputDir
#55
JeremyWesthead
closed
4 months ago
0
VERSION++
#54
JeremyWesthead
closed
4 months ago
0
Feat/table update script
#53
JeremyWesthead
closed
4 months ago
2
fix: ensure fasta adjudicated mutations get all predictions
#52
JeremyWesthead
closed
5 months ago
0
tuberculosis amr catalogues
#51
alantsangmb
closed
2 months ago
5
fix: use gumpy 1.2.6
#50
JeremyWesthead
closed
7 months ago
0
Fix/gzip python3.12
#49
JeremyWesthead
closed
8 months ago
0
Fix/avoid duplicate rrs
#48
JeremyWesthead
closed
8 months ago
0
Fix/fasta adj evidence
#47
JeremyWesthead
closed
8 months ago
0
Return gene position for fasta nucleotide nulls
#46
JeremyWesthead
closed
8 months ago
0
Include fasta adjudicated mutations in json
#45
JeremyWesthead
closed
8 months ago
1
Fix/ensure effects df
#44
JeremyWesthead
closed
8 months ago
0
Mypy fixes + ensure predictions.csv is populated by fasta adjudication
#43
JeremyWesthead
closed
8 months ago
0
Feat/fasta adjudication
#42
JeremyWesthead
closed
8 months ago
0
Feat/add evidence
#41
JeremyWesthead
closed
9 months ago
1
fix so predictions.csv still written even when no mutations detected
#40
philipwfowler
closed
9 months ago
0
Fix to use `None` values if vcf idx cannot be found (#36)
#39
JeremyWesthead
closed
9 months ago
0
Fix to ensure that multis aren't erroneously duplicated
#38
JeremyWesthead
closed
9 months ago
0
"All arrays must be of the same length"
#37
philipwfowler
closed
9 months ago
2
slightly different edge case where "index of the VCF evidence could not be determined!"
#36
philipwfowler
opened
9 months ago
2
Added error handling to temporarily appease oxfordmmm/gumpy#24
#35
JeremyWesthead
closed
10 months ago
0
`gene_name` --> `gene` in variants.csv for #33
#34
JeremyWesthead
closed
10 months ago
0
`gene` is called `gene_name` in `variants`
#33
philipwfowler
opened
10 months ago
1
Added s3fs req
#32
JeremyWesthead
closed
10 months ago
0
edge case where sample with minor alleles can't determine the index of the VCF evidence
#31
philipwfowler
closed
9 months ago
1
Added pushing to OCR as well as dockerhub for GPAS
#30
JeremyWesthead
closed
11 months ago
1
Add version flag
#29
JeremyWesthead
closed
11 months ago
0
OutdatedGumpyException
#28
alantsangmb
closed
11 months ago
3
gnomonicus version
#27
alantsangmb
closed
11 months ago
5
minor alleles incorrectly classified as dominant for `1/1` calls
#26
philipwfowler
closed
11 months ago
1
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