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56 Open 152 Closed
56 Open 152 Closed
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Issues list

Add "overwrite" functionality to Python API
#415 opened May 30, 2025 by hyanwong 0.1.7
2
Drop isolated_as_missing and contig_id arguments in tskit.convert
#413 opened May 28, 2025 by jeromekelleher
Documented VCZ writer API enhancement New feature or request
#412 opened May 23, 2025 by jeromekelleher
Add Python API for plink documentation Improvements or additions to documentation
#411 opened May 23, 2025 by jeromekelleher
Add memory control options to plink and tskit CLIs enhancement New feature or request
#410 opened May 23, 2025 by jeromekelleher
Optimise pandas usage for read_bim and read_fam enhancement New feature or request
#409 opened May 23, 2025 by jeromekelleher
Improve Python API documention documentation Improvements or additions to documentation
#407 opened May 23, 2025 by jeromekelleher
Add support for coordinate handling in tskit enhancement New feature or request
#405 opened May 23, 2025 by jeromekelleher
Review Format/Source API and make pickling requirements explicit enhancement New feature or request
#403 opened May 23, 2025 by jeromekelleher
Haploids inconsistently marked as phased/unphased
#399 opened May 22, 2025 by jeromekelleher
Add contig_length to plink output enhancement New feature or request
#394 opened May 21, 2025 by jeromekelleher
Add the "provisional reference" flag to plink output enhancement New feature or request
#393 opened May 21, 2025 by jeromekelleher
Add sample fields to plink conversion enhancement New feature or request
#392 opened May 21, 2025 by jeromekelleher
ALT and REF alleles incorrect in plink conversion
#391 opened May 20, 2025 by jeromekelleher
1
Compute ancestral states after tskit to zarr conversion enhancement New feature or request
#387 opened May 13, 2025 by duncanMR 0.1.7
4
Add AC and AN after tskit to zarr conversion enhancement New feature or request
#386 opened May 13, 2025 by duncanMR
1
Add option of zipping output of convert/encode enhancement New feature or request
#376 opened May 9, 2025 by jeromekelleher
VCF to VCZ encode zarr conversion leads to Disk Quota Exceeded (by generating a wild amount of files)
#366 opened May 6, 2025 by moshejasper
14
How to make a small zarr file from a large VCF?
#365 opened May 2, 2025 by hyanwong
3
Error on converting GWAS-VCF files bug Something isn't working
#345 opened Apr 6, 2025 by jeromekelleher
1
Empty VCFs not working bug Something isn't working
#342 opened Apr 3, 2025 by jeromekelleher
dencode cannot partition in samples dimension?
#341 opened Apr 2, 2025 by rajwanir
3
Document supported input formats for vcf2zarr and partitioning rules
#338 opened Mar 28, 2025 by jeromekelleher
Simulated tests broken on OSX intel because of msprime wheels
#336 opened Mar 19, 2025 by jeromekelleher
Refactor to reduce duplication across different input types
#333 opened Mar 17, 2025 by benjeffery
4
ProTip! Exclude everything labeled bug with -label:bug.