issues
search
dorbarker
/
voc-identify
Identify Variants of Concern from metagenomic samples of SARS-CoV-2
MIT License
12
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Output fails when using YAML files
#43
melohar
closed
3 years ago
1
add --input as synonym of --bam
#42
dorbarker
closed
3 years ago
0
cooccurrence_matrices/absolute lists wrong SNP
#41
ibseq
opened
3 years ago
7
Add support for SAM and CRAM files
#40
dorbarker
opened
3 years ago
1
fix name of pyyaml package
#39
dorbarker
closed
3 years ago
0
PHE mutations
#38
dorbarker
closed
3 years ago
0
Read PHE variant definitions directly
#37
dorbarker
closed
3 years ago
0
More informative error on failed mutations file parse
#36
dorbarker
closed
3 years ago
0
Dedup
#35
dorbarker
closed
3 years ago
0
Optionally save internal representation of results
#34
dorbarker
opened
3 years ago
0
running multiple bam files
#33
ibseq
closed
3 years ago
1
issue runnign snakemake workflow voc-identify.smk
#32
ibseq
closed
3 years ago
13
snakemake
#31
ibseq
closed
3 years ago
1
Reorg
#30
dorbarker
closed
3 years ago
0
Enhanced summary
#29
dorbarker
closed
3 years ago
0
Enhanced summary
#28
dorbarker
closed
3 years ago
0
Reorganize project
#27
dorbarker
closed
3 years ago
1
Fix deletion overlap
#26
dorbarker
closed
3 years ago
0
Deduplicate reads
#25
dorbarker
closed
3 years ago
0
Alternate subtitiutions
#24
dorbarker
closed
3 years ago
0
Cut memory use
#23
dorbarker
closed
3 years ago
0
Validate substitution and insertion format in mutations file at parse time
#22
dorbarker
closed
3 years ago
0
Insertions
#21
dorbarker
closed
3 years ago
0
Fix revcomp handling and refactor parsing
#20
dorbarker
closed
3 years ago
0
Handling of reverse complementation is probably broken
#19
dorbarker
closed
3 years ago
0
convert count of positions in a voc to bitarray
#18
dorbarker
closed
3 years ago
0
Qol
#17
dorbarker
closed
3 years ago
0
Fix miscalculation of read overlap for deletions
#16
dorbarker
closed
3 years ago
0
change alignment DF to Series
#15
dorbarker
closed
3 years ago
0
Clean up type hints
#14
dorbarker
closed
3 years ago
0
Add proportion of overlapping reads to read species
#13
dorbarker
closed
3 years ago
0
Dels and multibase
#12
dorbarker
closed
3 years ago
0
Dels and multibase
#11
dorbarker
closed
3 years ago
0
Output fails if VOC name has a forward slash in it
#10
dorbarker
closed
3 years ago
0
Illumina
#9
dorbarker
closed
3 years ago
0
Support Illumina reads
#8
dorbarker
closed
3 years ago
0
fix bug with rev comp reads
#7
dorbarker
closed
3 years ago
0
--delimiter CLI argument
#6
dorbarker
closed
3 years ago
0
Add test data
#5
dorbarker
closed
3 years ago
0
Create LICENSE
#4
dorbarker
closed
3 years ago
0
Support multi-base substitutions
#3
dorbarker
closed
3 years ago
0
Support point deletions
#2
dorbarker
closed
3 years ago
0
Mutation format
#1
dorbarker
closed
3 years ago
0