Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / tskit-dev/tsinfer issues and pull requests
#935 - Numpy 2.0 supporting release
Issue -
State: open - Opened by jeromekelleher 11 days ago
#934 - Grep for "sgkit" in names and replace
Issue -
State: open - Opened by jeromekelleher 11 days ago
#933 - Investigate AFS bias due to polytomies
Issue -
State: open - Opened by hyanwong 20 days ago
- 3 comments
#932 - Bring sample batch matching in line with ancestor matching
Issue -
State: open - Opened by benjeffery 20 days ago
#931 - Set node metadata schema
Pull Request -
State: open - Opened by hyanwong 24 days ago
- 2 comments
#930 - Allow the same scheme name, if description matches
Pull Request -
State: closed - Opened by hyanwong 25 days ago
- 7 comments
#929 - Overwriting md schema
Issue -
State: closed - Opened by hyanwong 25 days ago
#928 - Always read alleles as strings (not bytes)
Pull Request -
State: open - Opened by hyanwong 25 days ago
- 5 comments
Labels: AUTOMERGE-REQUESTED
#927 - Check all alleles at a site are unique before inference
Issue -
State: open - Opened by hyanwong 25 days ago
- 6 comments
Labels: bug
#926 - Add dependency on tsdate
Issue -
State: open - Opened by jeromekelleher 28 days ago
- 3 comments
Labels: enhancement
#925 - How to save an SgkitSampleData instance, e.g. for running the CLI
Issue -
State: open - Opened by hyanwong about 1 month ago
- 4 comments
#924 - Class method to create simple SgkitSampleData files for demos
Issue -
State: open - Opened by hyanwong about 1 month ago
- 1 comment
#923 - Add `ancestral_allele` and `variant_time` parameters to SgkitSampleData creator, with ability to provide numpy arrays
Issue -
State: open - Opened by hyanwong about 1 month ago
- 6 comments
#922 - Rename SgkitSampleData object?
Issue -
State: open - Opened by hyanwong about 1 month ago
#921 - Batch job ancestor matching.
Issue -
State: open - Opened by benjeffery about 1 month ago
- 3 comments
#920 - Reinstate 3.11, 3.12 testing after sgkit fix.
Issue -
State: open - Opened by benjeffery about 2 months ago
- 1 comment
#919 - Pin to zarr < 3
Issue -
State: open - Opened by jeromekelleher about 2 months ago
#918 - Fix CI
Pull Request -
State: closed - Opened by benjeffery about 2 months ago
- 4 comments
#917 - Batch ancestor matching
Pull Request -
State: open - Opened by benjeffery about 2 months ago
- 5 comments
#916 - Identifying PC nodes / edges added during match_samples
Issue -
State: open - Opened by hyanwong about 2 months ago
- 3 comments
#915 - SgkitSampleData.from_tree_sequence bugs out
Issue -
State: open - Opened by hyanwong 2 months ago
#914 - Fix OSX tests
Pull Request -
State: closed - Opened by benjeffery 2 months ago
- 1 comment
#913 - Low density regions and splitting
Issue -
State: open - Opened by benjeffery 3 months ago
- 2 comments
Labels: enhancement
#912 - Simplify dev reqs and make compatible with tsdate
Pull Request -
State: closed - Opened by benjeffery 3 months ago
- 1 comment
#911 - Improve ancestor building by using more information
Issue -
State: open - Opened by hyanwong 3 months ago
#910 - Tests: allow file closing to pass if name undefined
Pull Request -
State: closed - Opened by hyanwong 3 months ago
- 1 comment
#909 - Compiling on Apple ARM - mostly works
Issue -
State: closed - Opened by hyanwong 3 months ago
#908 - Tweak ma-match progressbar total
Pull Request -
State: closed - Opened by hyanwong 4 months ago
- 1 comment
#907 - Tests don't work unless you install the package
Issue -
State: closed - Opened by hyanwong 4 months ago
- 2 comments
#906 - Make tqdm work nicely in notebooks
Pull Request -
State: closed - Opened by hyanwong 4 months ago
- 14 comments
#905 - Makefile doesn't override CC if it already exists
Pull Request -
State: closed - Opened by hyanwong 4 months ago
- 1 comment
#904 - Compilation overrides CC
Issue -
State: closed - Opened by hyanwong 4 months ago
- 1 comment
#903 - Investigate why sample nodes attach to deep roots / ultimate ancestor
Issue -
State: open - Opened by hyanwong 5 months ago
- 20 comments
#902 - Update cli.py
Pull Request -
State: closed - Opened by hyanwong 5 months ago
- 1 comment
#901 - Add `mask` option to `insert_missing_sites`
Issue -
State: closed - Opened by benjeffery 5 months ago
- 1 comment
Labels: enhancement
#900 - Mask names
Pull Request -
State: closed - Opened by benjeffery 5 months ago
- 3 comments
#899 - Flip polarity
Pull Request -
State: closed - Opened by benjeffery 5 months ago
- 2 comments
#898 - Allow names of sample and variant maskes to be specified.
Issue -
State: open - Opened by benjeffery 5 months ago
#897 - Flip polarity of masks
Issue -
State: closed - Opened by benjeffery 5 months ago
- 1 comment
#896 - Add sample mask
Pull Request -
State: closed - Opened by benjeffery 5 months ago
- 14 comments
#895 - Sample masking from sgkit dataset
Issue -
State: open - Opened by benjeffery 5 months ago
- 1 comment
#894 - Why not append `None` to all reported SampleData allele lists?
Issue -
State: open - Opened by hyanwong 5 months ago
#893 - Corner case: cannot encode a SNP next to an indel in standard VCF encoding
Issue -
State: open - Opened by hyanwong 5 months ago
- 1 comment
#892 - SgkitSampleData format missing data bug
Issue -
State: open - Opened by hyanwong 5 months ago
- 2 comments
Labels: bug
#891 - Replace node_span in eval_util
Issue -
State: open - Opened by hyanwong 5 months ago
#890 - Add seed to simulate_genotype_call_dataset in tests
Issue -
State: open - Opened by hyanwong 5 months ago
#889 - Check duplicate positions
Pull Request -
State: closed - Opened by hyanwong 5 months ago
- 12 comments
#888 - SgkitSampleData allows duplicate positions
Issue -
State: closed - Opened by hyanwong 5 months ago
#887 - Better formatted error message for ancestral alleles
Pull Request -
State: closed - Opened by hyanwong 5 months ago
- 1 comment
#886 - Ancestor.inference_sites_set never used
Issue -
State: open - Opened by hyanwong 5 months ago
- 1 comment
#885 - Allow empty ancestral alleles
Pull Request -
State: closed - Opened by hyanwong 5 months ago
- 3 comments
#884 - "Empty alleles must be at the end" error for 1000G VCFs
Issue -
State: open - Opened by hyanwong 5 months ago
- 1 comment
#883 - SGkit equivalent for tutorial read_vcf
Issue -
State: open - Opened by hyanwong 5 months ago
- 5 comments
#881 - Set sample node times
Issue -
State: open - Opened by hyanwong 6 months ago
#880 - Batching during match ancestors wastes worker CPU.
Issue -
State: closed - Opened by benjeffery 6 months ago
- 3 comments
Labels: enhancement
#879 - Limit linesweep to 1M ancestors
Pull Request -
State: closed - Opened by benjeffery 6 months ago
- 2 comments
#878 - Don't double count progress
Pull Request -
State: closed - Opened by benjeffery 7 months ago
- 1 comment
#877 - Robustness of tsinfer & tsdate to selection
Issue -
State: open - Opened by hyanwong 7 months ago
- 23 comments
#876 - Parallel matching via batch jobs
Pull Request -
State: closed - Opened by benjeffery 8 months ago
- 4 comments
#875 - Error involving individual metadata when matching samples to an ancestors tree sequence
Issue -
State: open - Opened by szhan 8 months ago
- 1 comment
#874 - Sample matching progress bar incorrect
Issue -
State: open - Opened by benjeffery 8 months ago
- 1 comment
#873 - Fix OSX CI failures
Pull Request -
State: closed - Opened by benjeffery 8 months ago
- 6 comments
#872 - Return sgkit sample_id in individual metadata
Pull Request -
State: closed - Opened by benjeffery 8 months ago
- 5 comments
#871 - Record sgkit sample_ids in individual metadata
Issue -
State: closed - Opened by benjeffery 8 months ago
#870 - No sites used for inference
Issue -
State: open - Opened by bgyuris 8 months ago
- 4 comments
#868 - polytomies
Issue -
State: closed - Opened by frezaei98 8 months ago
- 1 comment
#867 - KC Distance of an inferred tree sequence
Issue -
State: closed - Opened by frezaei98 9 months ago
- 5 comments
#865 - Update docs build
Pull Request -
State: open - Opened by benjeffery 9 months ago
#864 - Update README.md
Pull Request -
State: closed - Opened by hyanwong 9 months ago
- 5 comments
#863 - Allowing fuzzy probabilities for ancestral state assignment, using an HMM
Issue -
State: open - Opened by hyanwong 10 months ago
- 1 comment
#862 - Document `map_additional_sites`` argument
Issue -
State: open - Opened by jeromekelleher 10 months ago
#861 - Make mapping additional sites optional
Pull Request -
State: closed - Opened by benjeffery 10 months ago
- 1 comment
#859 - Fix windows disk space
Pull Request -
State: closed - Opened by benjeffery 10 months ago
- 2 comments
#858 - Excessive RAM usage in the final stages of `match_samples`
Issue -
State: open - Opened by benjeffery 10 months ago
#857 - Parallelise mapping additional sites
Issue -
State: open - Opened by benjeffery 10 months ago
#856 - Switch to sphinx-book-theme
Pull Request -
State: closed - Opened by benjeffery 10 months ago
- 5 comments
#854 - Update deps and fix evaluation.py for new pandas
Pull Request -
State: closed - Opened by benjeffery 11 months ago
- 2 comments
#853 - Dask sample matching
Pull Request -
State: closed - Opened by benjeffery 11 months ago
- 3 comments
#852 - Update docs deps
Pull Request -
State: closed - Opened by benjeffery 11 months ago
#851 - Removing entirely unary nodes
Issue -
State: open - Opened by hyanwong 12 months ago
- 3 comments
#850 - Cut up root node (not just ultimate ancestor)
Issue -
State: open - Opened by hyanwong 12 months ago
- 5 comments
#849 - Rework sgkit ancestral allele
Pull Request -
State: closed - Opened by benjeffery 12 months ago
- 6 comments
#848 - Ancestral alleles from VCF
Issue -
State: open - Opened by hyanwong 12 months ago
- 1 comment
#847 - Hard error on missing sgkit ancestral state
Issue -
State: closed - Opened by benjeffery 12 months ago
- 1 comment
#846 - Ancestral allele handling
Issue -
State: open - Opened by benjeffery 12 months ago
- 1 comment
#845 - Add more tests to ancestral_allele fetching
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#844 - Update installation.rst
Pull Request -
State: closed - Opened by eaton-lab about 1 year ago
- 1 comment
#842 - Save mismatch ratio in provenance
Pull Request -
State: closed - Opened by hyanwong about 1 year ago
- 9 comments
#841 - Tutorial on creating Sample File from VCF giving error
Issue -
State: closed - Opened by Tatianabellagio about 1 year ago
- 6 comments
#840 - Add "Inferring large datasets" documentation
Issue -
State: open - Opened by benjeffery about 1 year ago
#839 - Add `AncestorData` diagnostic plots function.
Issue -
State: open - Opened by benjeffery about 1 year ago
- 1 comment
#838 - Split large ancestor groups up for both caching and dask scheduling.
Issue -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#837 - Fetch ancestors within dask worker
Issue -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#836 - Improve ancestor fetching
Issue -
State: open - Opened by benjeffery about 1 year ago
#835 - Add resume for sample matching
Issue -
State: open - Opened by benjeffery about 1 year ago
#834 - Document resume option
Issue -
State: open - Opened by benjeffery about 1 year ago
#833 - Fix circleCI meson error
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#832 - Circle CI failure
Issue -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#831 - Docs: clarify alleles list with missing data
Pull Request -
State: closed - Opened by hyanwong about 1 year ago
- 8 comments
#830 - Refactor low-level code
Pull Request -
State: open - Opened by jeromekelleher about 1 year ago
- 2 comments