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astheeggeggs
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lshmm
code to run Li and Stephens
MIT License
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Lower parameter values for `ts_larger` when testing diploid Viterbi
#93
szhan
closed
2 weeks ago
0
Fix get_examples_haploid
#92
szhan
closed
2 weeks ago
0
Fix `get_examples_haploid`
#91
szhan
closed
2 weeks ago
0
Check number of copiable entries in reference genotype matrix
#90
szhan
closed
2 weeks ago
2
Require numpy 1.x
#89
szhan
closed
2 weeks ago
0
Require numpy 1.x
#88
szhan
closed
2 weeks ago
1
Check the number of copiable entries per site in reference panel
#87
szhan
closed
2 weeks ago
3
Remove all-NONCOPY ancestors
#86
szhan
closed
2 weeks ago
0
Implement a naive diploid Viterbi algorithm to run on "merged" ancestral haplotypes
#85
szhan
opened
3 weeks ago
5
Investigate `get_ancestral_haplotypes` in `lsbase.py`
#84
szhan
closed
2 weeks ago
2
Modify r/n to vary along the sites when partial ancestors are present
#83
szhan
closed
3 weeks ago
0
Check input haplotypes
#82
szhan
closed
3 weeks ago
0
Check for `MISSING` and `NONCOPY` values in input data
#81
szhan
closed
3 weeks ago
0
Split test files
#80
szhan
closed
3 weeks ago
0
Numba-fy functions to get emission probability matrix
#79
szhan
closed
3 weeks ago
0
Computing `r/n` when partial ancestral haplotypes are in reference panel
#78
szhan
closed
3 weeks ago
3
API functions to run over multiple input queries
#77
szhan
opened
3 weeks ago
1
Refactor check_inputs
#76
szhan
closed
3 weeks ago
2
Fix get_examples_diploid
#75
szhan
closed
3 weeks ago
1
Fix `get_examples_diploid`
#74
szhan
closed
3 weeks ago
0
Reduce time to run tests
#73
szhan
closed
3 weeks ago
2
Refactor get_emission_matrix_haploid
#72
szhan
closed
3 weeks ago
0
Remove redundant lines in get_example_pars
#71
szhan
closed
3 weeks ago
0
Add tests for `set_emission_probabilities` when `prob_mutation` is not specified
#70
szhan
closed
2 weeks ago
1
Speed up `get_emission_matrix_haploid` and `get_emission_matrix_diploid` using Numba
#69
szhan
closed
3 weeks ago
0
Refactor `get_emission_matrix_haploid`
#68
szhan
closed
3 weeks ago
0
Remove redundant lines in `get_examples_pars`
#67
szhan
closed
3 weeks ago
0
Rename variables in functions assigning emission probabilities for diploid case
#66
szhan
closed
3 weeks ago
1
Reduce run time for tests for diploid Viterbi implementations
#65
szhan
opened
1 month ago
5
Implement NONCOPY for the diploid case
#64
szhan
closed
1 month ago
5
Split tests for the haploid and diploid cases into separate files
#63
szhan
closed
3 weeks ago
0
Add tests for scaling mutation rates in the haploid case
#62
szhan
closed
1 month ago
0
Scale mutation rate for the diploid case and add tests
#61
szhan
closed
1 month ago
5
Modify set_emission_probabilities
#60
szhan
closed
1 month ago
0
Implement mutation rate scaling for diploid case and add tests
#59
szhan
closed
1 month ago
2
Implement NONCOPY for the diploid case
#58
szhan
closed
1 month ago
0
Convert haplotypes to genotypes for query
#57
szhan
closed
1 month ago
1
Convert haplotypes to genotypes for query
#56
szhan
closed
1 month ago
8
Scale mutation rates for the diploid case
#55
szhan
closed
1 month ago
1
Replace query when getting examples for haploid case
#54
szhan
closed
1 month ago
1
Write up README for the haploid case
#53
szhan
closed
2 weeks ago
1
Add parameters to control when to pass extreme parameter values to tests
#52
szhan
closed
1 month ago
1
Control when extreme parameter values are passed to tests
#51
szhan
closed
1 month ago
0
Add a function to convert haplotypes to genotypes
#50
szhan
closed
1 month ago
0
Add convert haplotypes to genotypes
#49
szhan
closed
1 month ago
1
Function to convert reference haplotypes to genotypes in diploid case
#48
szhan
closed
1 month ago
0
Rename variables in the functions for setting emission probabilities for diploid case
#47
szhan
closed
3 weeks ago
0
Replace all missing query with mostly all missing query in get_examples_haploid
#46
szhan
closed
1 month ago
2
Refactor and improve `check_inputs`
#45
szhan
closed
3 weeks ago
8
Fix get examples for diploid case
#44
szhan
closed
1 month ago
5
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