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szhan
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tsimpute
Genome-wide genotype imputation using tree sequences.
MIT License
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Add mutations after adding new individuals to a tree sequence
#144
szhan
opened
1 year ago
1
Package LS HMM sample path vis tool
#143
szhan
closed
1 year ago
0
Add progress bar
#142
szhan
closed
1 year ago
0
Rewrote add_individual_to_tree_sequence
#141
szhan
closed
1 year ago
0
Append a bunch of sample edges at once to an existing tree sequence
#140
szhan
closed
1 year ago
0
Keep adding new samples to an existing ts
#139
szhan
closed
1 year ago
0
Look into source code of BEAGLE 4.1
#138
szhan
closed
1 year ago
3
Refactor `make_compatible_genotypes` and update tests
#137
szhan
closed
1 year ago
0
Refactor `make_compatible_genotypes`
#136
szhan
closed
1 year ago
0
Visualise sample paths interactively using `bokeh` in `Jupyter` notebooks
#135
szhan
closed
1 year ago
0
Do not add binary chars to allale list
#134
szhan
closed
1 year ago
0
Refactor add_individual_to_tree_sequence
#133
szhan
closed
1 year ago
0
Copy contig_length when making compatible genotypes
#132
szhan
closed
1 year ago
0
Add `contig_length` when making compatible genotypes
#131
szhan
closed
1 year ago
0
Move `prepare_ancestral_states.sh`
#130
szhan
closed
1 year ago
0
Freeze 'SamplePath' instances
#129
szhan
closed
1 year ago
1
Make `is_valid` in class `SamplePath` an attribute
#128
szhan
closed
1 year ago
0
Make `is_valid` in `SamplePath` a class attribute
#127
szhan
closed
1 year ago
1
Add simple example for writing VCF from augmented tree sequence
#126
szhan
closed
1 year ago
1
Update tests for `SamplePath`
#125
szhan
closed
1 year ago
0
Turn off `numba` when running tests on `get_matching_indices`
#124
szhan
opened
1 year ago
0
Refactor `add_individual_to_tree_sequence`
#123
szhan
closed
1 year ago
1
Add tests for `write_vcf` from tree sequences augmented by `add_individual_to_tree_sequence`
#122
szhan
opened
1 year ago
0
Add tests for `add_individual_to_tree_sequence`
#121
szhan
closed
1 year ago
1
Fix bugs with `add_individual_to_tree_sequence`
#120
szhan
closed
1 year ago
0
Parallelise `remap_genotypes` using a threaded map
#119
szhan
closed
1 year ago
0
Add a single edge when there is no switch
#118
szhan
closed
1 year ago
0
Fix bugs introduced when making changes to `SamplePath`
#117
szhan
closed
1 year ago
0
Fix bug where data type int8 is too small, leading to overflow
#116
szhan
closed
1 year ago
0
Show progress bar for step 1
#115
szhan
closed
1 year ago
0
Minor reformatting and cleanup
#114
szhan
closed
1 year ago
0
Keep VCF header when making compatible genotypes
#113
szhan
closed
1 year ago
1
Add function to parallelise runs of a function
#112
szhan
closed
1 year ago
0
Check variant alleles from `remap_genotypes`
#111
szhan
closed
1 year ago
0
Pass `Typed.List` to `get_matching_indices`
#110
szhan
opened
1 year ago
2
Fix tests
#109
szhan
closed
1 year ago
0
Clean up and reorganise
#108
szhan
closed
1 year ago
0
Fix bugs in prepare_input_matrix
#107
szhan
closed
1 year ago
0
Parallelise `get_traceback_path`
#106
szhan
opened
1 year ago
5
Show progress bar for `remap_genotypes`
#105
szhan
closed
1 year ago
0
Speed up `remap_genotypes` by using `numba`
#104
szhan
closed
1 year ago
1
Replace binary characters with regular characters
#103
szhan
closed
1 year ago
0
Scale up `get_matching_indices`
#102
szhan
closed
1 year ago
2
Fix bug in make_compatible_genotypes
#101
szhan
closed
1 year ago
0
Rework `impute_by_sample_matching`
#100
szhan
closed
1 year ago
1
Rework `impute_by_sample_matching` so that it doesn't take `SampleData` anymore
#99
szhan
closed
1 year ago
0
Improve function to add an individual to an existing tree sequence
#98
szhan
closed
1 year ago
2
Allow for adding sample paths of an individual to an existing tree sequence
#97
szhan
closed
1 year ago
2
Add tests for `add_individual_to_tree_sequence`
#96
szhan
closed
1 year ago
2
Functions to facilitate VCF comparison using sgkit
#95
szhan
closed
1 year ago
10
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