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cov-lineages
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scorpio
serious constellations of reoccurring phylogenetically-independent origin
GNU General Public License v3.0
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Dev
#51
rmcolq
closed
10 months ago
0
Tidy and add tests
#50
rmcolq
closed
1 year ago
0
XBB.1 misclassified as XBB in Singapore in samples after 2022-10-10
#49
mg14
opened
1 year ago
0
Pangolin v1.12 as used by GISAID misclassifies a lot of true BA.5* as BA.2*
#48
corneliusroemer
opened
1 year ago
2
hundred XM genomes called as 'Unassigned' or as BA.1
#46
akifoss
closed
1 year ago
5
Scorpio: Many BA.4/5 misclassified as BA.2* because "Probable Omicron (BA.2-like)"
#47
corneliusroemer
opened
2 years ago
26
Scorpio overriding UShER calls for XD recombinants
#45
SVN-PhD
opened
2 years ago
1
handle recombinant assignments that dont pass both parents- dont acce…
#44
aineniamh
closed
2 years ago
0
Dev
#43
rmcolq
closed
1 year ago
0
Handle multiple levels of definition within a constellation
#42
rmcolq
closed
2 years ago
0
Giving input file without `-i` causes stack trace
#41
rambaut
closed
2 years ago
0
Add check that scorpio file is compatible with current scorpio version
#40
rambaut
opened
2 years ago
0
add option to skip translation to aa
#39
rmcolq
closed
2 years ago
0
Dev
#38
rmcolq
closed
2 years ago
0
Make scorpio multithreaded
#37
rmcolq
closed
2 years ago
0
Allow mutation strings to have comments at the end (if this doesn't work already)
#36
rambaut
closed
2 years ago
1
Allow a constellation to have different levels of rules for e.g. probable cases rather than certain cases
#35
rmcolq
closed
2 years ago
0
small bug fixes
#34
rmcolq
closed
2 years ago
0
fastq as input data
#33
carlottaolivero
closed
2 years ago
1
scorpio overriding AY.4.2 to B.1.617.2 on very few Ns
#32
mcroxen
closed
2 years ago
12
Dev
#31
rmcolq
closed
2 years ago
0
Enable multiple constellation files for the same "constellation"
#30
rmcolq
closed
2 years ago
1
Allow for a rule with more flexibility for indels
#29
rmcolq
closed
2 years ago
2
Fix bugs with define
#28
rmcolq
closed
2 years ago
0
Dev
#27
rmcolq
closed
2 years ago
0
Do a 'union' haplotype of multiple definition files.
#26
rambaut
closed
2 years ago
1
For `haplotype` command only use one directory of constellation files.
#25
rambaut
closed
2 years ago
2
Dev
#24
rmcolq
closed
2 years ago
0
Dev
#23
rmcolq
closed
3 years ago
0
Allow mutations to be specified on command line for scorpio haplotype
#22
rmcolq
closed
3 years ago
0
Scorpio version reporting 0.3.5 incorrectly (?)
#21
jacaravas
closed
3 years ago
1
merge in dev
#20
rmcolq
closed
3 years ago
0
Dev
#19
rmcolq
closed
3 years ago
1
Mutation information
#18
santoshe1
closed
3 years ago
2
Dev
#17
rmcolq
closed
3 years ago
0
Dev
#16
rmcolq
closed
3 years ago
0
Bug in scorpio
#15
animesh-workplace
closed
3 years ago
9
Merge in dev
#14
rmcolq
closed
3 years ago
0
Improve deletion handling
#13
rmcolq
closed
3 years ago
0
Handle changed constellation labels
#12
rmcolq
closed
3 years ago
0
Add option to output other labels (i.e., --who-label and --phe-label
#11
rmcolq
closed
3 years ago
0
Create an optional interspersion statistic
#10
rmcolq
opened
3 years ago
0
Add a list of problematic sites and provide a warning if one comes back as reference
#9
rmcolq
closed
2 years ago
1
CDS orf1a at position 741 is L, but reference sequence has F
#8
tseemann
closed
3 years ago
6
Enable protein based mutation definitions e.g. NSP1
#7
rmcolq
closed
3 years ago
0
Add option to include additional mutation calls from a mutations CSV when classifying
#6
rmcolq
closed
3 years ago
0
Add command line args for intermediate thresholds for `define`
#5
rmcolq
closed
3 years ago
0
In `define` output intermediates in nice format
#4
rmcolq
closed
3 years ago
0
Allow outgroups to be specified when running `define`
#3
rmcolq
closed
3 years ago
0
Use support when classifying to choose the constellation with best support
#2
rmcolq
closed
3 years ago
0
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