astheeggeggs lshmm issues

astheeggeggs / lshmm

code to run Li and Stephens

MIT License

4 stars 3 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Add test for path switching at sites where recombination rate is positive

#146 szhan closed 4 months ago
0
Add tests for known breakpoints in Viterbi paths

#145 szhan closed 4 months ago
0
Explain diploid LS HMM in README

#144 szhan opened 4 months ago
0
Update notebook to reflect API changes

#143 szhan closed 4 months ago
0
Support multiple allelic states

#142 szhan opened 4 months ago
1
Add argument to pass function to define emission probabilities for haploid case

#141 szhan closed 4 months ago
0
Refactor tests for haploid case with multiallelic sites

#140 szhan closed 4 months ago
0
Allow for invariant sites in input data

#139 szhan closed 4 months ago
0
Remove requiring the first value of input recombination probability array be zero

#138 szhan closed 4 months ago
0
Allow for invariant sites in the input data

#137 szhan closed 4 months ago
0
First value of input recombination probabilities need not be zero

#136 szhan closed 4 months ago
0
Pre-release `0.0.7`

#135 szhan closed 4 months ago
0
Change API functions to take query sequences of unphased genotypes

#134 szhan closed 4 months ago
0
Change query input to API

#133 szhan closed 4 months ago
1
Rework check_inputs to no longer take num_alleles

#132 szhan closed 4 months ago
0
Refactor setting default of scale_mutation_rate

#131 szhan closed 4 months ago
0
Rework `check_inputs` to take user-specified ploidy instead of inferring it from input

#130 szhan closed 4 months ago
0
Implement a naive haploid Viterbi algorithm to run on "merged" ancestral haplotypes

#129 szhan opened 4 months ago
0
Rework `check_inputs`

#128 szhan closed 4 months ago
1
Refactor functions to simulate test data

#127 szhan closed 4 months ago
0
Refactor functions to simulate test data

#126 szhan closed 4 months ago
2
Backward incompatibility in API functions in `0.0.8`

#125 szhan closed 4 months ago
4
Add Jupyter notebook showing how to use haploid LS HMM algorithms

#124 szhan closed 4 months ago
0
Add a Jupyter notebook to demo the main API functions for the haploid case

#123 szhan closed 4 months ago
0
Fix bug when adding extreme recombination probabilities

#122 szhan closed 4 months ago
0
Fix bug in `get_examples_pars` when adding extreme rates

#121 szhan closed 4 months ago
0
Check that first value in recomb. prob. array is zero

#120 szhan closed 4 months ago
0
Check the first value in recombination probability array

#119 szhan closed 4 months ago
1
First item in input recombination probability must be zero

#118 szhan closed 4 months ago
1
Update pyproject.toml

#117 szhan closed 4 months ago
0
Clean up to pip install locally

#116 szhan closed 4 months ago
0
Remove old package from setup config

#115 szhan closed 4 months ago
0
README

#114 szhan closed 4 months ago
0
Pre-release checks

#113 szhan closed 4 months ago
0
Rework get_examples_*

#112 szhan closed 4 months ago
0
Raise errors instead of asserting

#111 szhan closed 4 months ago
0
Split tests by algorithm

#110 szhan closed 4 months ago
0
Rework `get_examples_haploid` and `get_examples_diploid`

#109 szhan closed 4 months ago
0
Check that the number of haplotypes meets a minimum

#108 szhan closed 4 months ago
0
Check number of haplotypes when using `estimate_mutation_probability`

#107 szhan closed 4 months ago
0
Add tests when prob_mutation is not specified

#106 szhan closed 4 months ago
2
Separate tests by Viterbi versus forward-backward algorithm

#105 szhan closed 4 months ago
0
Refactor how mutation probability is defined when not specified

#104 szhan closed 4 months ago
0
Refactor how mutation probability is set when `prob_mutation` is set to `None`

#103 szhan closed 4 months ago
2
Pre-release 0.0.6

#102 szhan closed 4 months ago
3
Raise errors instead of asserting in `core.py`

#101 szhan closed 4 months ago
0
Clean up docstrings in vit_haploid.py

#100 szhan closed 4 months ago
0
Refactor function to get emission probability in the haploid case

#99 szhan closed 4 months ago
1
Refactor `get_emission_probability_haploid` and `get_index_in_emission_matrix_haploid`

#98 szhan closed 4 months ago
1
Reorganise functions in core

#97 szhan closed 4 months ago
0