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AlphaGenes
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AlphaPeel
AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
MIT License
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"reference" is not included in documentation
#127
AprilYUZhang
opened
10 months ago
1
Update tests for the changes of the option names in #122
#126
XingerTang
closed
10 months ago
4
add output for ".rec_prob.txt" in PeelingIO.py
#125
AprilYUZhang
opened
10 months ago
0
Modify est_alt_allele_prob part of test_est
#124
XingerTang
opened
10 months ago
0
What does e=1e-06 in peelingInfo.segregationTensorXY = ProbMath.generateSegregationXYChrom(e=1e-06) mean?
#123
gregorgorjanc
opened
10 months ago
0
Stage_2
#122
AprilYUZhang
closed
9 months ago
25
Devel-stage 2
#121
AprilYUZhang
closed
10 months ago
6
Remove double brackets in documentation
#120
XingerTang
opened
11 months ago
1
Changing more argument names
#119
AprilYUZhang
closed
11 months ago
4
Update tinyhouse based on recent bugfix & check if our tests would capture the same error
#118
gregorgorjanc
opened
11 months ago
2
Change the file format of genotype probabilities file?
#117
gregorgorjanc
opened
11 months ago
0
Rename -call_phase to -hap #89 and dosages to dosage #90
#115
AprilYUZhang
closed
11 months ago
5
changing parameters to model parameters #91
#114
AprilYUZhang
closed
11 months ago
0
Update tests according to the changes in the options names and file names
#113
XingerTang
closed
3 months ago
4
What does the peeling option -nophasefounders do?
#112
gregorgorjanc
opened
11 months ago
1
Rename peeling options -runtype, -ncycles, and -maxthreads
#111
gregorgorjanc
closed
8 months ago
1
Rename output arguments -out, -writekey, -onlykeyed, -iothreads
#110
gregorgorjanc
closed
8 months ago
1
Rename input file arguments -pedigree, -genotypes, -seqfile, -bfile
#109
gregorgorjanc
closed
8 months ago
2
Rename -startsnp to -start_snp and -stopsnp to -stop_snp
#108
gregorgorjanc
closed
8 months ago
1
Polish -sexchrom to -sex_chrom
#107
gregorgorjanc
closed
8 months ago
1
Polish hybrid file arguments -mapfile, -segmapfile, and -segfile
#106
gregorgorjanc
closed
8 months ago
1
changed no_dosages to no_dosage #90
#105
AprilYUZhang
closed
11 months ago
1
Rename the -esterrors and -estmaf
#104
gregorgorjanc
closed
8 months ago
1
Rename the -length argument in relation to recombination
#103
gregorgorjanc
closed
8 months ago
1
Rename -error to -geno_error_prob and -seqerror to -seq_error_prob?
#102
gregorgorjanc
closed
8 months ago
1
Add option for more than one chromosome
#101
gregorgorjanc
opened
11 months ago
0
Clarify outputkey
#100
gregorgorjanc
closed
11 months ago
1
Issues for the Oct. 09 meeting
#99
AprilYUZhang
closed
11 months ago
1
we should not output segragation prob as default
#98
AprilYUZhang
closed
10 months ago
0
consolidate model parameter filenames
#97
AprilYUZhang
closed
8 months ago
0
rename output seg to seg_prob
#96
AprilYUZhang
closed
10 months ago
0
rename -no_seg to -no_seq_prob
#95
AprilYUZhang
closed
11 months ago
1
Add an extension `.txt` for all text output files
#94
XingerTang
opened
11 months ago
0
add option to output genotype prob
#93
AprilYUZhang
closed
10 months ago
0
rename -haps to -phased_geno_prob
#92
AprilYUZhang
closed
10 months ago
2
rename parameter files section to Model parameters in the docs
#91
AprilYUZhang
closed
11 months ago
4
rename -no_dosages to -no_dosage
#90
AprilYUZhang
closed
11 months ago
5
rename -call_phase option to -hap
#89
AprilYUZhang
closed
11 months ago
4
update description of -seqerror
#88
AprilYUZhang
closed
12 months ago
4
Add NEWS/Changelog file to summarise key changes between versions
#87
gregorgorjanc
opened
1 year ago
4
Add new test files for the accuracy tests and Update tests for the new option names
#86
XingerTang
closed
11 months ago
17
Can we account for sequence read quality scores?
#85
gregorgorjanc
opened
1 year ago
0
Implement max-product / Viterbi algorithm
#84
gregorgorjanc
opened
1 year ago
0
Add test_onlykeyed for half-founders
#83
XingerTang
closed
1 year ago
1
Fix the bug of writeCalledPhase()
#82
XingerTang
closed
8 months ago
5
Improve functional tests
#81
XingerTang
closed
1 year ago
1
Add accuracy test for other output in addition to allele dosage
#80
gregorgorjanc
opened
1 year ago
6
Add Sex Information to Pedigree File
#79
XingerTang
opened
1 year ago
0
Test cross-architectures
#78
XingerTang
opened
1 year ago
0
Update the version of numba required
#77
XingerTang
opened
1 year ago
0
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