magicDGS thaplv issues - Githubissues

magicDGS / thaplv

Tools for Haploid/Haplotype VCFs

BSD 3-Clause "New" or "Revised" License

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GetFasta should use the FastaWriter in GATK

#55 magicDGS opened 7 years ago
0
GetFasta using intervals

#54 magicDGS opened 7 years ago
1
Improve tests for multi-thread when using heuristic statistics

#53 magicDGS opened 8 years ago
0
Command line proper validation + simpler Main

#52 magicDGS closed 8 years ago
1
Validate arguments with customCommandLineValidation

#51 magicDGS closed 8 years ago
1
Extend Main from GATK4 for simplify code

#50 magicDGS closed 8 years ago
2
Removed DONT_CHECK in favor of CHECK_ONLY

#49 magicDGS closed 8 years ago
1
Port LDdecay

#48 magicDGS closed 8 years ago
1
Clean implementation of LDdecay

#47 magicDGS opened 8 years ago
0
LDdecay filter for MAF

#46 magicDGS opened 8 years ago
0
LDdecay outputs all the SNP pairs computed

#45 magicDGS opened 8 years ago
1
Reorganizing tests

#44 magicDGS closed 8 years ago
1
RunningStats should use exact impementations until a limit is reached

#43 magicDGS opened 8 years ago
0
Should LengthBinning.formatBins output bins with not data?

#42 magicDGS opened 8 years ago
0
Synchronization implementations

#41 magicDGS opened 8 years ago
0
Decide LDdecay default quantiles to compute

#40 magicDGS opened 8 years ago
0
Binning 0 r correlation issue

#39 magicDGS opened 8 years ago
0
Change codecov thresholds

#38 magicDGS opened 8 years ago
0
Tune codecov threshold before alpha

#37 magicDGS closed 8 years ago
1
Allele vector implementation

#36 magicDGS closed 8 years ago
1
Change coverage report to Codecov

#35 magicDGS closed 8 years ago
1
Code cleaning + Codacy badge

#34 magicDGS closed 8 years ago
5
LD components

#33 magicDGS closed 8 years ago
2
Change coverage report to Codecov

#32 magicDGS closed 8 years ago
0
Updated dependencies, gradle and jacoco versions

#31 magicDGS closed 8 years ago
2
Use VariantWalkerBase in our HaplotypeWalker

#30 magicDGS opened 8 years ago
1
Implement memoizer for some functions

#29 magicDGS opened 8 years ago
0
Update GATK4 for new functionality

#28 magicDGS closed 8 years ago
0
Implemented ReferenceSimilarity

#27 magicDGS closed 8 years ago
3
Availables sites computed in PairwiseDifferencesWindow could be wrong

#26 magicDGS opened 8 years ago
0
Allow selecting/excluding samples from tools

#25 magicDGS opened 8 years ago
0
Don't include windows with 0 variants at the end of processing in IBDOutput

#24 magicDGS opened 8 years ago
0
No reference for IBDcompute

#23 magicDGS opened 8 years ago
0
Port ImputeKNN and finish implementation

#22 magicDGS opened 8 years ago
0
Port LDdecay

#21 magicDGS closed 8 years ago
0
Port ReferenceSimilarity

#20 magicDGS closed 8 years ago
2
Added IBDcompute + tests

#19 magicDGS closed 8 years ago
4
Updated GATK4 dependency

#18 magicDGS closed 8 years ago
2
GetFasta should/could have an option to include indels

#17 magicDGS opened 8 years ago
0
Reference methods for distance pairs should be changed

#16 magicDGS opened 8 years ago
0
Update GATK4 dependency

#15 magicDGS closed 8 years ago
1
Ported GetFasta

#14 magicDGS closed 8 years ago
3
Added distance pairs implementation

#13 magicDGS closed 8 years ago
5
Fixing license in test files

#12 magicDGS closed 8 years ago
0
Fix LICENSE

#11 magicDGS closed 8 years ago
1
Implement BCI haplotype calling

#10 magicDGS opened 8 years ago
1
DONT_CHECK HaplotypeModel should be changed for eventual checks and throw error

#9 magicDGS closed 8 years ago
0
email in LICENSE is wrongly formatted

#8 magicDGS closed 8 years ago
0
Implement other HaplotypeModels

#7 magicDGS opened 8 years ago
0
ConvertHaplotypes allele subsetting

#6 magicDGS opened 8 years ago
0