AlphaGenes AlphaPeel issues

AlphaGenes / AlphaPeel

AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees

MIT License

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issues

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Improve the algorithm of the main peeling function

#169 XingerTang opened 5 days ago
0
Recombination map initialization with partial chromosome

#168 XingerTang opened 1 week ago
0
Build functionality to input phased data

#167 AprilYUZhang opened 3 weeks ago
1
Documentation update for Alternative Allele Frequencies Output

#166 RosCraddock opened 3 weeks ago
0
implement Viterbi on segregation prob

#165 AprilYUZhang opened 1 month ago
23
Mutation rate in AlphaPeel

#164 XingerTang opened 1 month ago
3
Some confusions for the code in Peeling.py

#163 AprilYUZhang closed 1 month ago
8
Formula modificaiton for the estimation of recombinaiton rate

#162 AprilYUZhang opened 2 months ago
21
Do we need to add base population inbreeding coefficient?

#161 gregorgorjanc opened 3 months ago
0
Can we estimate effect of some other factors on genotype and allele probabilities?

#160 gregorgorjanc opened 3 months ago
0
Update Change Log for new metafounders and alternative allele frequencies functionality.

#159 RosCraddock opened 5 months ago
0
Add changelog #87

#158 XingerTang opened 5 months ago
0
fix bug related to argument and output

#157 AprilYUZhang closed 3 weeks ago
1
Develop functional tests for alt_allele_prob_file and est_alt_allele_prob with multiple metafounders

#156 XingerTang closed 3 weeks ago
3
Ensure map file input is handled properly when not sorted in ascending order

#155 XingerTang opened 5 months ago
1
Provide map file input option for non-hybrid mode #153

#154 XingerTang closed 5 months ago
5
Provide map file for non-hybrid mode

#153 XingerTang opened 5 months ago
0
Documentation update - Issue #149, and #151

#152 RosCraddock closed 5 months ago
7
Add option to name the first metafounder

#151 RosCraddock opened 6 months ago
0
Develop tests for alt_allele_prob_file and est_alt_allele_prob with multiple metafounders

#150 XingerTang opened 6 months ago
3
Update documentation for the user-defined input of alternative allele frequency

#149 XingerTang opened 6 months ago
1
Estimation of allele freq with metafounders

#148 XingerTang opened 6 months ago
3
Consolidate storing maf between PeelingInfo and Pedigree

#147 XingerTang opened 6 months ago
1
Set default hap threshold and default geno threshold

#146 XingerTang opened 6 months ago
2
Estimate rec_prob

#145 XingerTang opened 6 months ago
1
Add rec_prob input and output

#144 XingerTang opened 6 months ago
10
Check all the arguements and design logic tests

#143 AprilYUZhang opened 6 months ago
0
Implement alt_allele_prob option

#142 AprilYUZhang opened 6 months ago
6
Implement logic test adding seq data

#141 AprilYUZhang closed 3 weeks ago
0
Implement logic test adding pedigree error test

#140 AprilYUZhang closed 3 weeks ago
0
Implement logic test 04 adding genotype error test

#139 AprilYUZhang closed 3 weeks ago
0
Implement logic test 03 adding recombination

#138 AprilYUZhang closed 3 weeks ago
0
Implement logic test 02: Test basic phasing

#137 AprilYUZhang closed 3 weeks ago
0
Implement logic test 01: Test basic phasing

#136 AprilYUZhang closed 3 weeks ago
0
print out seq-error-prob.txt only when sequence data used

#135 AprilYUZhang opened 6 months ago
0
remove empty line from geno_prob.txtv and phased_geno_prob.txt

#134 AprilYUZhang opened 6 months ago
0
-geno not producing outputfile

#133 AprilYUZhang opened 6 months ago
0
-hap not producing output file

#132 AprilYUZhang opened 6 months ago
0
Update test for option phasefile & allow longer test name in test report

#131 XingerTang closed 7 months ago
8
Update tests for the changes of the option names in #122 Part 2

#130 XingerTang closed 7 months ago
8
In documentation and code help statements change animals to individuals

#129 gregorgorjanc opened 7 months ago
1
rename ".called." in writeBinaryCalledGenotypes

#128 AprilYUZhang opened 7 months ago
0
"reference" is not included in documentation

#127 AprilYUZhang opened 7 months ago
1
Update tests for the changes of the option names in #122

#126 XingerTang closed 7 months ago
4
add output for ".rec_prob.txt" in PeelingIO.py

#125 AprilYUZhang opened 7 months ago
0
Modify est_alt_allele_prob part of test_est

#124 XingerTang opened 7 months ago
0
What does e=1e-06 in peelingInfo.segregationTensorXY = ProbMath.generateSegregationXYChrom(e=1e-06) mean?

#123 gregorgorjanc opened 7 months ago
0
Stage_2

#122 AprilYUZhang closed 6 months ago
25
Devel-stage 2

#121 AprilYUZhang closed 7 months ago
6
Remove double brackets in documentation

#120 XingerTang opened 8 months ago
1