issues
search
ksumngs
/
HapLink.jl
Viral haplotype calling by linkage disequilibrium
https://ksumngs.github.io/HapLink.jl
MIT License
0
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Release v1.1.0
#63
MillironX
closed
8 months ago
1
docs: Polish docs
#62
MillironX
closed
8 months ago
1
perf: Add bounds for haplotype matrix
#61
MillironX
closed
8 months ago
0
perf: Use sparse matrices for haplotype calling
#60
MillironX
closed
8 months ago
0
CompatHelper: bump compat for Automa to 1, (keep existing compat)
#59
github-actions[bot]
opened
1 year ago
0
CompatHelper: bump compat for FASTX to 2, (keep existing compat)
#58
github-actions[bot]
opened
1 year ago
0
CompatHelper: bump compat for Automa to 0.8, (keep existing compat)
#57
github-actions[bot]
opened
1 year ago
0
chore: Downgrade FASTX compat to v1
#56
MillironX
closed
1 year ago
1
TagBot trigger issue
#55
JuliaTagBot
closed
1 year ago
2
Release v1.0.0
#54
MillironX
closed
1 year ago
0
feat: Add Nix config
#53
MillironX
closed
1 year ago
0
Docs
#52
MillironX
closed
1 year ago
0
CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat)
#51
github-actions[bot]
opened
1 year ago
0
CompatHelper: add new compat entry for Comonicon at version 1, (keep existing compat)
#50
github-actions[bot]
closed
1 year ago
0
Only output simulation settings when using simulated reads
#49
MillironX
closed
1 year ago
0
Implement Comonicon.jl interface
#48
MillironX
closed
1 year ago
0
CompatHelper: bump compat for GenomicFeatures to 3, (keep existing compat)
#47
github-actions[bot]
opened
1 year ago
0
fix: Add `haplink sequences` back into CLI
#46
MillironX
closed
1 year ago
0
feat: Add Earthfile for documentation builds
#45
MillironX
closed
1 year ago
0
[Feature]: Documentation
#44
MillironX
closed
1 year ago
0
[Bug]: Add `haplink sequences` command back
#43
MillironX
closed
1 year ago
0
[Feature]: Add Earthfile for testing and docs
#42
MillironX
closed
1 year ago
1
[Feature]: Add Nix configuration
#41
MillironX
closed
1 year ago
0
[Feature]: Separate raw and ml haplotype calling into separate commands
#40
MillironX
closed
1 year ago
0
[Feature]: Add to Bioconda
#39
MillironX
closed
8 months ago
1
[Feature]: Use Commonicon.jl for CLI
#38
MillironX
closed
1 year ago
0
[FIX]: Correct calculations for linkage disequilibrium and Chi-squared test
#37
MillironX
closed
1 year ago
0
Replace Husky with pre-commit
#36
MillironX
closed
1 year ago
0
Feature/sequence variation.jl rewrite
#35
MillironX
closed
1 year ago
0
CompatHelper: bump compat for XAM to 0.3, (keep existing compat)
#34
github-actions[bot]
closed
1 year ago
0
CompatHelper: bump compat for BioAlignments to 3, (keep existing compat)
#33
github-actions[bot]
closed
1 year ago
1
CompatHelper: bump compat for FASTX to 2, (keep existing compat)
#32
github-actions[bot]
closed
1 year ago
1
Remove unicode character from VCF header
#31
MillironX
closed
2 years ago
0
Feature/consensus-haplotypes
#30
MillironX
closed
2 years ago
0
Add command for consensus sequence generation
#29
MillironX
closed
2 years ago
0
[Feature]: Add option to keep filtered variants in VCF output
#28
MillironX
closed
1 year ago
1
[Feature]: Call haplotypes based on the consensus sequence
#27
MillironX
closed
2 years ago
0
[Feature]: Add consensus sequence generator
#26
MillironX
closed
2 years ago
0
Add haplotype names to YAML haplotype output
#25
MillironX
closed
2 years ago
0
[Feature]: Implement in pure Julia
#24
MillironX
closed
1 year ago
1
[Feature]: Use standard in/out
#23
MillironX
opened
2 years ago
1
[Feature]: Process genomes with multiple segments/chromosomes
#22
MillironX
closed
1 year ago
1
[Feature]: Random seed parameter
#21
MillironX
closed
2 years ago
1
Use Pkg's Artifact API to install `bam-readcount` automatically
#20
MillironX
closed
2 years ago
0
CompatHelper: bump compat for BioSequences to 3, (keep existing compat)
#19
github-actions[bot]
closed
1 year ago
1
Add overlapping reads matching algorithm
#18
MillironX
closed
2 years ago
0
[Feature]: Find all possible paths via alignment
#17
MillironX
closed
2 years ago
0
Find haplotypes on long reads without ML
#16
MillironX
closed
2 years ago
0
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)
#15
github-actions[bot]
closed
1 year ago
1
CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat)
#14
github-actions[bot]
closed
2 years ago
0
Next