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szhan
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tsimpute
Genome-wide genotype imputation using tree sequences.
MIT License
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Function to compare genotypes stored in `xarray.dataset` using `sgkit`
#94
szhan
opened
1 year ago
7
Split `prepare_dataset.ipynb` into separate notebooks
#93
szhan
closed
1 year ago
1
Remove None when making alternate alleles string if in allele list
#92
szhan
closed
1 year ago
1
Switch order of checks
#91
szhan
closed
1 year ago
0
Check allele list sizes before traversing the data structures
#90
szhan
closed
1 year ago
0
Print num_case_2d
#89
szhan
closed
1 year ago
0
Print info instead of logging to file
#88
szhan
closed
1 year ago
1
Raise ValueError instead of asserting
#87
szhan
closed
1 year ago
0
Fix docstring and comments
#86
szhan
closed
1 year ago
0
Allow for processing of tree sequence
#85
szhan
closed
1 year ago
0
Fix bug where flipped alleles is not passed correctly
#84
szhan
closed
1 year ago
0
Fix assertion
#83
szhan
closed
1 year ago
0
Handle cases where a site is monoallelic in sd
#82
szhan
closed
1 year ago
0
Raise TypeError when sd is not SampleData and/or ts is not TreeSequence
#81
szhan
closed
1 year ago
0
bgzip is needed, not gzip
#80
szhan
closed
1 year ago
0
Remove assertion of sequence length
#79
szhan
closed
1 year ago
0
Fix bug in convert.py where the last entry in a VCF file is not processed
#78
szhan
closed
1 year ago
0
Write to gzipped VCF file
#77
szhan
closed
1 year ago
0
More minor things
#76
szhan
closed
1 year ago
0
Add some comments
#75
szhan
closed
1 year ago
0
Fix bug where sites_position is not accessed as a numpy array but zarr
#74
szhan
closed
1 year ago
0
Make is_compatible take SampleData or TreeSequence
#73
szhan
closed
1 year ago
0
Missing data should not be considered when comparing allele lists
#72
szhan
closed
1 year ago
0
Add routine to check compatibility between SampleData and TreeSequence
#71
szhan
closed
1 year ago
0
Package routines
#70
szhan
opened
1 year ago
1
Add sample edges properly instead of squashing edges
#69
szhan
closed
1 year ago
0
Plot IQS versus MAF
#68
szhan
closed
1 year ago
0
Visualise imputation performance
#67
szhan
opened
1 year ago
2
Add plot visually comparing sample paths
#66
szhan
closed
1 year ago
0
Visualise sample paths in context of additional info
#65
szhan
closed
1 year ago
0
Visualise LS HMM copying paths
#64
szhan
closed
1 year ago
14
Fix shell script to prepare ancestral state files
#63
szhan
closed
1 year ago
0
Remove unused files
#62
szhan
closed
1 year ago
0
Remove unused code
#61
szhan
closed
1 year ago
0
Make it required to provide contig name
#60
szhan
closed
1 year ago
0
Remove automatic position adjustment
#59
szhan
closed
1 year ago
0
Remove unused code
#58
szhan
closed
1 year ago
0
Move print_samples_to_vcf to utils
#57
szhan
closed
1 year ago
0
Clean up and remove assertion
#56
szhan
closed
1 year ago
0
Remove unused code
#55
szhan
closed
1 year ago
0
Fix bug
#54
szhan
closed
1 year ago
0
Fix bug concerning ploidy assignment
#53
szhan
closed
1 year ago
0
Update metadata correctly
#52
szhan
closed
1 year ago
0
Fix calls when chip_site_pos and/or mask_site_pos are not specified
#51
szhan
closed
1 year ago
0
Update env YAML file
#50
szhan
closed
1 year ago
0
Move plot_mmr_analysis.py
#49
szhan
closed
1 year ago
0
Add population when making compatible samples
#48
szhan
closed
1 year ago
0
Remove unnecessary code
#47
szhan
closed
1 year ago
0
Shorten variable names
#46
szhan
closed
1 year ago
0
Continue to remove unused code
#45
szhan
closed
1 year ago
0
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