tskit-dev/tsinfer issues and pull requests

#874 - Sample matching progress bar incorrect

Issue - State: open - Opened by benjeffery about 1 year ago - 1 comment

#873 - Fix OSX CI failures

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 6 comments

#872 - Return sgkit sample_id in individual metadata

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 5 comments

#871 - Record sgkit sample_ids in individual metadata

Issue - State: closed - Opened by benjeffery about 1 year ago

#870 - No sites used for inference

Issue - State: open - Opened by bgyuris about 1 year ago - 4 comments

#868 - polytomies

Issue - State: closed - Opened by frezaei98 about 1 year ago - 1 comment

#867 - KC Distance of an inferred tree sequence

Issue - State: closed - Opened by frezaei98 about 1 year ago - 5 comments

#865 - Update docs build

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 1 comment

#864 - Update README.md

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 5 comments

#863 - Allowing fuzzy probabilities for ancestral state assignment, using an HMM

Issue - State: open - Opened by hyanwong about 1 year ago - 1 comment

#862 - Document `map_additional_sites`` argument

Issue - State: open - Opened by jeromekelleher about 1 year ago

#861 - Make mapping additional sites optional

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 1 comment

#859 - Fix windows disk space

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 2 comments

#858 - Excessive RAM usage in the final stages of `match_samples`

Issue - State: open - Opened by benjeffery about 1 year ago

#857 - Parallelise mapping additional sites

Issue - State: open - Opened by benjeffery about 1 year ago

#856 - Switch to sphinx-book-theme

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 5 comments

#854 - Update deps and fix evaluation.py for new pandas

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#853 - Dask sample matching

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#852 - Update docs deps

Pull Request - State: closed - Opened by benjeffery over 1 year ago

#851 - Removing entirely unary nodes

Issue - State: open - Opened by hyanwong over 1 year ago - 3 comments

#850 - Cut up root node (not just ultimate ancestor)

Issue - State: open - Opened by hyanwong over 1 year ago - 5 comments

#849 - Rework sgkit ancestral allele

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 6 comments

#848 - Ancestral alleles from VCF

Issue - State: closed - Opened by hyanwong over 1 year ago - 2 comments

#847 - Hard error on missing sgkit ancestral state

Issue - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#846 - Ancestral allele handling

Issue - State: open - Opened by benjeffery over 1 year ago - 2 comments

#845 - Add more tests to ancestral_allele fetching

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#844 - Update installation.rst

Pull Request - State: closed - Opened by eaton-lab over 1 year ago - 1 comment

#842 - Save mismatch ratio in provenance

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 9 comments

#841 - Tutorial on creating Sample File from VCF giving error

Issue - State: closed - Opened by Tatianabellagio over 1 year ago - 6 comments

#840 - Add "Inferring large datasets" documentation

Issue - State: open - Opened by benjeffery over 1 year ago

#839 - Add `AncestorData` diagnostic plots function.

Issue - State: open - Opened by benjeffery over 1 year ago - 1 comment

#838 - Split large ancestor groups up for both caching and dask scheduling.

Issue - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#837 - Fetch ancestors within dask worker

Issue - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#836 - Improve ancestor fetching

Issue - State: open - Opened by benjeffery over 1 year ago

#835 - Add resume for sample matching

Issue - State: open - Opened by benjeffery over 1 year ago

#834 - Document resume option

Issue - State: open - Opened by benjeffery over 1 year ago

#833 - Fix circleCI meson error

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#832 - Circle CI failure

Issue - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#831 - Docs: clarify alleles list with missing data

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 8 comments

#830 - Refactor low-level code

Pull Request - State: open - Opened by jeromekelleher over 1 year ago - 2 comments

#829 - Start on factoring out ResultBuffer

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 10 comments

#828 - Add linesweep ancestor grouping

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 11 comments

#827 - Resume using LMDB

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 7 comments

#826 - Store resume buffer of match results

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 2 comments

#825 - match_epoch function

Issue - State: open - Opened by jeromekelleher over 1 year ago

#824 - Checkpointing for ancestor and sample matching

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 2 comments

#823 - Disable phase checks

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 2 comments

#822 - Python 3.11 support

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 8 comments

#821 - Package tsinfer for pyodide

Issue - State: closed - Opened by benjeffery over 1 year ago - 10 comments

#820 - Fix codecov

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#819 - Need a bugfix release for zarr issue

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 2 comments

#818 - Dask experiments

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 4 comments

#817 - Out-of-core ancestor matching

Issue - State: open - Opened by benjeffery over 1 year ago

#816 - Speed up bit unpacking in `generate_ancestors`

Issue - State: open - Opened by benjeffery over 1 year ago - 1 comment

#815 - Add two-bit encoding for generate ancestors

Issue - State: open - Opened by jeromekelleher over 1 year ago - 4 comments
Labels: enhancement

#814 - Zero recombination rate, reprise

Issue - State: open - Opened by hyanwong over 1 year ago - 1 comment

#813 - Update mergify

Pull Request - State: closed - Opened by benjeffery over 1 year ago

#812 - Pass through options to tqdm

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 4 comments

#811 - Don't load all ancestors when truncating

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 6 comments

#810 - Default SGkit alleles are byte strings, which confuses tsinfer:

Issue - State: closed - Opened by hyanwong over 1 year ago - 2 comments

#809 - One-bit encoding for genotypes

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 31 comments

#808 - Alloc genotype memory from mmap

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 11 comments

#807 - WIP - Match samples in parallel

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 1 comment

#806 - Ancestor generation requires entire genotype array to be in-memory.

Issue - State: closed - Opened by benjeffery almost 2 years ago - 10 comments

#805 - Fix lint

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 1 comment

#804 - Write only the extent of ancestors to improve generation perf

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 1 comment

#803 - Add tute code to compare orig and inferred variation

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#802 - Fix dep specification

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#800 - `sgkit` ancestral allele

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 3 comments

#799 - Values of recombination and mismatch rate

Issue - State: open - Opened by frezaei98 almost 2 years ago - 6 comments

#798 - Tidy eval util

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#796 - Installation currently fails under python 3.11 due to numba dep

Issue - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#795 - Fix doc build

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#794 - Filter out empty string alleles

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 9 comments

#793 - Match chunks of samples

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 2 comments

#792 - Variant.alleles needs to filter out empty string for sgkit

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#791 - Add mask to sgkit SampleData

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 4 comments

#790 - Circle CI failure

Issue - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#789 - Fix doc build

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 1 comment

#788 - Doc build failure

Issue - State: closed - Opened by benjeffery almost 2 years ago
Labels: documentation

#786 - sgkit: Support `call_genotype_mask`?

Issue - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#785 - Correct length of sites metadata

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 1 comment

#784 - Error if sgkit sample data is unphased

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 4 comments

#783 - Change SgkitSampleData to accept a path or store.

Issue - State: closed - Opened by benjeffery almost 2 years ago - 3 comments

#782 - Testing CI

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#781 - Fix and update pre-commit

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 3 comments

#780 - Fix docs build

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 2 comments

#779 - Decouple SampleData from AncestorData

Pull Request - State: closed - Opened by benjeffery about 2 years ago - 5 comments

#778 - Sgkit compatible ancestors

Pull Request - State: closed - Opened by benjeffery about 2 years ago - 21 comments

#777 - Remove "extend" code (ported to sc2ts)

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 2 comments

#776 - Parsimoniously explain direct reversions

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 3 comments

#775 - Remove pytest-xdist

Pull Request - State: closed - Opened by benjeffery about 2 years ago - 5 comments

#774 - Tutorial tweaks

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 3 comments

#773 - Run tests sequentially

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment

#772 - sgkit: Error/Warning on unphased data when ploidy > 1.

Issue - State: closed - Opened by benjeffery about 2 years ago - 3 comments

#771 - CI: windows tests failing with parallel running

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 3 comments

#770 - Tweak for CPU time change

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 6 comments

#769 - Fix numpy pip

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 4 comments

#768 - Extend greedy mutation coalescing

Pull Request - State: closed - Opened by jeromekelleher about 2 years ago - 6 comments

#767 - sgkit: Workflow documentation

Issue - State: open - Opened by benjeffery about 2 years ago - 1 comment

GitHub / tskit-dev/tsinfer issues and pull requests