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astheeggeggs
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lshmm
code to run Li and Stephens
MIT License
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Add test for path switching at sites where recombination rate is positive
#146
szhan
closed
2 months ago
0
Add tests for known breakpoints in Viterbi paths
#145
szhan
closed
2 months ago
0
Explain diploid LS HMM in README
#144
szhan
opened
2 months ago
0
Update notebook to reflect API changes
#143
szhan
closed
3 months ago
0
Support multiple allelic states
#142
szhan
opened
3 months ago
1
Add argument to pass function to define emission probabilities for haploid case
#141
szhan
closed
3 months ago
0
Refactor tests for haploid case with multiallelic sites
#140
szhan
closed
3 months ago
0
Allow for invariant sites in input data
#139
szhan
closed
3 months ago
0
Remove requiring the first value of input recombination probability array be zero
#138
szhan
closed
3 months ago
0
Allow for invariant sites in the input data
#137
szhan
closed
3 months ago
0
First value of input recombination probabilities need not be zero
#136
szhan
closed
3 months ago
0
Pre-release `0.0.7`
#135
szhan
closed
3 months ago
0
Change API functions to take query sequences of unphased genotypes
#134
szhan
closed
3 months ago
0
Change query input to API
#133
szhan
closed
3 months ago
1
Rework check_inputs to no longer take num_alleles
#132
szhan
closed
3 months ago
0
Refactor setting default of scale_mutation_rate
#131
szhan
closed
3 months ago
0
Rework `check_inputs` to take user-specified ploidy instead of inferring it from input
#130
szhan
closed
3 months ago
0
Implement a naive haploid Viterbi algorithm to run on "merged" ancestral haplotypes
#129
szhan
opened
3 months ago
0
Rework `check_inputs`
#128
szhan
closed
3 months ago
1
Refactor functions to simulate test data
#127
szhan
closed
3 months ago
0
Refactor functions to simulate test data
#126
szhan
closed
3 months ago
2
Backward incompatibility in API functions in `0.0.8`
#125
szhan
closed
3 months ago
4
Add Jupyter notebook showing how to use haploid LS HMM algorithms
#124
szhan
closed
3 months ago
0
Add a Jupyter notebook to demo the main API functions for the haploid case
#123
szhan
closed
3 months ago
0
Fix bug when adding extreme recombination probabilities
#122
szhan
closed
3 months ago
0
Fix bug in `get_examples_pars` when adding extreme rates
#121
szhan
closed
3 months ago
0
Check that first value in recomb. prob. array is zero
#120
szhan
closed
3 months ago
0
Check the first value in recombination probability array
#119
szhan
closed
3 months ago
1
First item in input recombination probability must be zero
#118
szhan
closed
3 months ago
1
Update pyproject.toml
#117
szhan
closed
3 months ago
0
Clean up to pip install locally
#116
szhan
closed
3 months ago
0
Remove old package from setup config
#115
szhan
closed
3 months ago
0
README
#114
szhan
closed
3 months ago
0
Pre-release checks
#113
szhan
closed
3 months ago
0
Rework get_examples_*
#112
szhan
closed
3 months ago
0
Raise errors instead of asserting
#111
szhan
closed
3 months ago
0
Split tests by algorithm
#110
szhan
closed
3 months ago
0
Rework `get_examples_haploid` and `get_examples_diploid`
#109
szhan
closed
3 months ago
0
Check that the number of haplotypes meets a minimum
#108
szhan
closed
3 months ago
0
Check number of haplotypes when using `estimate_mutation_probability`
#107
szhan
closed
3 months ago
0
Add tests when prob_mutation is not specified
#106
szhan
closed
3 months ago
2
Separate tests by Viterbi versus forward-backward algorithm
#105
szhan
closed
3 months ago
0
Refactor how mutation probability is defined when not specified
#104
szhan
closed
3 months ago
0
Refactor how mutation probability is set when `prob_mutation` is set to `None`
#103
szhan
closed
3 months ago
2
Pre-release 0.0.6
#102
szhan
closed
3 months ago
3
Raise errors instead of asserting in `core.py`
#101
szhan
closed
3 months ago
0
Clean up docstrings in vit_haploid.py
#100
szhan
closed
3 months ago
0
Refactor function to get emission probability in the haploid case
#99
szhan
closed
3 months ago
1
Refactor `get_emission_probability_haploid` and `get_index_in_emission_matrix_haploid`
#98
szhan
closed
3 months ago
1
Reorganise functions in core
#97
szhan
closed
3 months ago
0
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