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PlantandFoodResearch
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MCHap
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
MIT License
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Remove KMERCOV
#134
timothymillar
closed
2 years ago
1
Low memory version of exact calling method returns incorrect posterior mode probability
#133
timothymillar
closed
2 years ago
1
F/128 simplify input parameters
#132
timothymillar
closed
2 years ago
0
Default to error rate published by Pfeiffer et al 2018 #127
#131
timothymillar
closed
2 years ago
0
Add python 3.8 and 3.9 to build matrix #122
#130
timothymillar
closed
2 years ago
0
F/125 improve prior pmf
#129
timothymillar
closed
2 years ago
0
Simplify input parameters
#128
timothymillar
closed
2 years ago
1
Default to constant base error rate
#127
timothymillar
closed
2 years ago
0
Temperature gradiaent for parallel-temporing
#126
timothymillar
opened
2 years ago
0
Simplify PMF for calling Gibbs sampler
#125
timothymillar
closed
2 years ago
1
Remove use of factorial in prior probability function
#124
timothymillar
closed
2 years ago
0
Document an example workflow for calling haplotypes in a mapping population
#123
timothymillar
closed
1 year ago
0
Test against newer Python version
#122
timothymillar
closed
2 years ago
1
Documentation
#121
timothymillar
opened
2 years ago
4
Allow specification of population prior allele frequencies with mchap call
#120
timothymillar
closed
2 years ago
1
Create LICENSE
#119
kiwiroy
closed
2 years ago
0
Version 0.5.1
#118
timothymillar
closed
3 years ago
0
Integer overflow caused by use of in8 for alleles in greedy_caller
#117
timothymillar
closed
3 years ago
1
Option to use previous call as initial genotype when re-calling
#116
timothymillar
opened
3 years ago
0
Final alt allele count includeds counts of null allleles
#115
timothymillar
closed
3 years ago
1
Unifiy posterior mode methods
#114
timothymillar
opened
3 years ago
0
Drop zero-count alleles
#113
timothymillar
closed
2 years ago
3
Version 0.5.0
#112
timothymillar
closed
3 years ago
0
Unify exact calling methods
#111
timothymillar
opened
3 years ago
0
Seperate haplotype assembly and re-calling into two seperate tools.
#110
timothymillar
closed
3 years ago
1
Asub example
#109
timothymillar
closed
3 years ago
0
Version 0.4.2
#108
timothymillar
closed
3 years ago
0
Generalise default and per sample specification of parameters
#107
timothymillar
opened
3 years ago
0
F/version 0.4.1
#106
timothymillar
closed
3 years ago
0
Add CIGAR string for variants.
#105
timothymillar
opened
3 years ago
0
Re-calculate posterior with MCMC
#104
timothymillar
closed
3 years ago
1
Posterior allele frequencies
#103
timothymillar
closed
2 years ago
2
Remove optional fields from VCF when they aren't used.
#102
timothymillar
closed
3 years ago
1
Remove FORMAT/FT field from header
#101
timothymillar
closed
3 years ago
1
Version 0.4.0
#100
timothymillar
closed
3 years ago
0
Enable parrallel tempering on a per sample basis
#99
timothymillar
closed
3 years ago
1
Remove or INFO/AD and FORMAT/AD fields
#98
timothymillar
closed
3 years ago
3
Consider option to calculate log-likelihoods ignoring dosage for VCF output
#97
timothymillar
opened
3 years ago
0
Less stringent filtering
#96
timothymillar
closed
3 years ago
1
Option to report likelihoods in GL VCF field
#95
timothymillar
closed
3 years ago
0
Cache Numba compiled functions
#94
timothymillar
closed
3 years ago
1
Inclusion of alt alleles for recording posterior distributions in VCF output
#93
timothymillar
closed
3 years ago
1
Set default for --filter-probability to 0.90
#92
timothymillar
closed
3 years ago
1
Tag as Beta
#91
timothymillar
closed
3 years ago
0
Investigate HTPC friendly method for parallelisation
#90
timothymillar
closed
3 years ago
3
Record unknown/novel alleles
#89
timothymillar
opened
3 years ago
1
Improved exception handling
#88
timothymillar
closed
3 years ago
0
B/no reads or snps
#87
timothymillar
closed
3 years ago
0
B/no reads or snps
#86
timothymillar
closed
3 years ago
0
F/83 deduplicate reads
#85
timothymillar
closed
3 years ago
0
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