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jeromekelleher
/
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Rough version of max-daily-samples
#44
jeromekelleher
closed
1 year ago
0
bRecombinant nodes
#43
jeromekelleher
closed
1 year ago
0
Fix zero samples bug
#42
jeromekelleher
closed
1 year ago
0
Refactor matching code path
#41
jeromekelleher
closed
1 year ago
0
Deal with missing alignmnets
#40
jeromekelleher
closed
1 year ago
0
Missing files
#39
jeromekelleher
closed
1 year ago
0
Work with alignments directly
#38
jeromekelleher
closed
1 year ago
0
Refactor: change import-fasta fasta-to-zarr
#37
jeromekelleher
closed
1 year ago
1
Fix up some annoyances and clarify masked_sites value
#36
jeromekelleher
closed
1 year ago
0
Inference refactor
#35
jeromekelleher
closed
1 year ago
0
Fix cli --no-progress flags
#34
jeromekelleher
opened
1 year ago
0
Add masked_samples to site metadata
#33
jeromekelleher
closed
1 year ago
1
Add debug metadata to internal nodes
#32
jeromekelleher
closed
1 year ago
1
Rename QC metadata keys
#31
jeromekelleher
closed
1 year ago
1
Delete trailing values from datetimes
#30
jeromekelleher
closed
1 year ago
0
Add missing file
#29
jeromekelleher
closed
1 year ago
0
Fix ancestral state error
#28
jeromekelleher
closed
1 year ago
0
Mask missing flanks
#27
jeromekelleher
closed
1 year ago
0
Pass on extra params to tsinfer
#26
jeromekelleher
closed
1 year ago
0
Improve infer
#25
jeromekelleher
closed
1 year ago
0
Skip and warn for strains with no metadata
#24
jeromekelleher
closed
1 year ago
0
Move to Fasta data input
#23
jeromekelleher
closed
1 year ago
0
Add reference sequence
#22
jeromekelleher
opened
1 year ago
1
Add gene annotations to ts metadata
#21
jeromekelleher
opened
1 year ago
1
Rename to sc2ts
#20
jeromekelleher
closed
1 year ago
0
Add cli option to write log to file
#19
jeromekelleher
closed
1 year ago
0
Added max_submission_delay option
#18
jeromekelleher
closed
1 year ago
0
Rename import command
#17
jeromekelleher
closed
1 year ago
0
Add provenance support
#16
jeromekelleher
closed
1 year ago
0
Batch of improvements.
#15
jeromekelleher
closed
1 year ago
0
Add validate cli command
#14
jeromekelleher
closed
1 year ago
0
Basic changes needed for including initial state
#13
jeromekelleher
closed
1 year ago
0
Improve conversion perf (a bit)
#12
jeromekelleher
closed
1 year ago
0
Fix progress display
#11
jeromekelleher
closed
1 year ago
0
Force input to use ACGT allele encoding
#10
jeromekelleher
closed
1 year ago
0
Gvcf input fixed
#9
jeromekelleher
closed
1 year ago
0
Gvcf input
#8
jeromekelleher
closed
1 year ago
0
Update to use num_mismatches parameterisation
#7
jeromekelleher
closed
2 years ago
0
Added debug output and update on missing data
#6
jeromekelleher
closed
2 years ago
0
Make data ingest more robust
#5
jeromekelleher
closed
2 years ago
0
Use tsinfer extend
#4
jeromekelleher
closed
2 years ago
0
Add split samples command
#3
jeromekelleher
closed
2 years ago
0
Test file missing
#2
jeromekelleher
closed
2 years ago
0
Initial data prep
#1
jeromekelleher
closed
2 years ago
0
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