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
#829 - Start on factoring out ResultBuffer
Pull Request -
State: closed - Opened by jeromekelleher about 1 year ago
- 10 comments
#828 - Add linesweep ancestor grouping
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 11 comments
#827 - Resume using LMDB
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 7 comments
#826 - Store resume buffer of match results
Issue -
State: closed - Opened by jeromekelleher about 1 year ago
- 2 comments
#825 - match_epoch function
Issue -
State: open - Opened by jeromekelleher about 1 year ago
#824 - Checkpointing for ancestor and sample matching
Issue -
State: closed - Opened by jeromekelleher about 1 year ago
- 2 comments
#823 - Disable phase checks
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 2 comments
#822 - Python 3.11 support
Pull Request -
State: open - Opened by benjeffery about 1 year ago
- 7 comments
#821 - Package tsinfer for pyodide
Issue -
State: closed - Opened by benjeffery about 1 year ago
- 10 comments
#820 - Fix codecov
Pull Request -
State: closed - Opened by benjeffery about 1 year ago
- 1 comment
#819 - Need a bugfix release for zarr issue
Issue -
State: closed - Opened by jeromekelleher about 1 year ago
- 2 comments
#818 - Dask experiments
Pull Request -
State: closed - Opened by benjeffery about 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: open - 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 over 1 year ago
- 10 comments
#805 - Fix lint
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 1 comment
#804 - Write only the extent of ancestors to improve generation perf
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 1 comment
#803 - Add tute code to compare orig and inferred variation
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 1 comment
#802 - Fix dep specification
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 2 comments
#800 - `sgkit` ancestral allele
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 3 comments
#799 - Values of recombination and mismatch rate
Issue -
State: open - Opened by frezaei98 over 1 year ago
- 6 comments
#798 - Tidy eval util
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 1 comment
#796 - Installation currently fails under python 3.11 due to numba dep
Issue -
State: open - Opened by hyanwong over 1 year ago
- 1 comment
#795 - Fix doc build
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
#794 - Filter out empty string alleles
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 9 comments
#793 - Match chunks of samples
Issue -
State: open - Opened by jeromekelleher over 1 year ago
- 2 comments
#792 - Variant.alleles needs to filter out empty string for sgkit
Issue -
State: closed - Opened by jeromekelleher over 1 year ago
#791 - Add mask to sgkit SampleData
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 4 comments
#790 - Circle CI failure
Issue -
State: closed - Opened by benjeffery over 1 year ago
- 2 comments
#789 - Fix doc build
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 1 comment
#788 - Doc build failure
Issue -
State: closed - Opened by benjeffery over 1 year ago
Labels: documentation
#786 - sgkit: Support `call_genotype_mask`?
Issue -
State: closed - Opened by benjeffery over 1 year ago
- 2 comments
#785 - Correct length of sites metadata
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 1 comment
#784 - Error if sgkit sample data is unphased
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 4 comments
#783 - Change SgkitSampleData to accept a path or store.
Issue -
State: open - Opened by benjeffery over 1 year ago
- 2 comments
#782 - Testing CI
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 2 comments
#781 - Fix and update pre-commit
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 3 comments
#780 - Fix docs build
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 2 comments
#779 - Decouple SampleData from AncestorData
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 5 comments
#778 - Sgkit compatible ancestors
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 21 comments
#777 - Remove "extend" code (ported to sc2ts)
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 2 comments
#776 - Parsimoniously explain direct reversions
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 3 comments
#775 - Remove pytest-xdist
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 5 comments
#774 - Tutorial tweaks
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 3 comments
#773 - Run tests sequentially
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 1 comment
#772 - sgkit: Error/Warning on unphased data when ploidy > 1.
Issue -
State: closed - Opened by benjeffery over 1 year ago
- 3 comments
#771 - CI: windows tests failing with parallel running
Issue -
State: closed - Opened by jeromekelleher over 1 year ago
- 3 comments
#770 - Tweak for CPU time change
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 6 comments
#769 - Fix numpy pip
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 4 comments
#768 - Extend greedy mutation coalescing
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 6 comments
#767 - sgkit: Workflow documentation
Issue -
State: open - Opened by benjeffery over 1 year ago
- 1 comment
#766 - sgkit: Warn when default content for a missing dataset array is used.
Issue -
State: open - Opened by benjeffery over 1 year ago
#765 - sgkit: Error out on multiple contigs
Issue -
State: open - Opened by benjeffery over 1 year ago
#764 - sgkit: Use ancestral_allele_index
Issue -
State: closed - Opened by benjeffery over 1 year ago
#763 - sgkit: Use sequence length from dataset
Issue -
State: open - Opened by benjeffery over 1 year ago
- 1 comment
#762 - Add info logging during "extend" setup
Issue -
State: open - Opened by jeromekelleher over 1 year ago
#761 - Release traceback memory if gets > 2GiB
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 4 comments
#760 - Remove the "virtual-root-like" ancestor requirement from L&S matching
Issue -
State: open - Opened by hyanwong over 1 year ago
#759 - Do not require ancestors tree sequence to define internal nodes as samples
Issue -
State: open - Opened by hyanwong over 1 year ago
#758 - Update CHANGELOG.md
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 1 comment
#757 - Fix readme MIME for PyPI
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 1 comment
#756 - 0.3.0 pypi upload failed
Issue -
State: closed - Opened by jeromekelleher over 1 year ago
- 5 comments
Labels: bug
#755 - Update changelog for release
Pull Request -
State: closed - Opened by jeromekelleher over 1 year ago
- 1 comment
#754 - Add --keep-intermediates CLI option
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 10 comments
#753 - Allow msprime.RateMap or equivalent to be used in pip installs
Issue -
State: open - Opened by hyanwong over 1 year ago
- 8 comments
#752 - Temporarily disable --recombination-map in cli
Pull Request -
State: closed - Opened by hyanwong over 1 year ago
- 3 comments
#751 - Windows install fails because of msprime
Issue -
State: closed - Opened by jeromekelleher over 1 year ago
- 5 comments
Labels: bug
#748 - Minimum viable sgkit dataset
Pull Request -
State: closed - Opened by benjeffery over 1 year ago
- 28 comments
#739 - Variant method to return actual states
Issue -
State: open - Opened by hyanwong over 1 year ago
- 4 comments
#729 - Unify SampleData and AncestorsData file formats
Issue -
State: open - Opened by jeromekelleher over 1 year ago
- 2 comments
#728 - SampleData frontend for sgkit/xarray dataset
Issue -
State: closed - Opened by jeromekelleher over 1 year ago
- 4 comments
#707 - How to stop people getting confused when inspecting ancestors tree sequences?
Issue -
State: open - Opened by hyanwong almost 2 years ago
- 1 comment
#701 - Set individuals table metadata schema to permissive_json
Issue -
State: open - Opened by hyanwong almost 2 years ago
- 2 comments
#699 - Document SampleData attributes
Issue -
State: closed - Opened by szhan almost 2 years ago
- 2 comments
#696 - Allow sample data and ancestors files to store their time units
Issue -
State: open - Opened by hyanwong almost 2 years ago
- 8 comments
#688 - Document numpy array accessors in the sample data files?
Issue -
State: closed - Opened by hyanwong about 2 years ago
- 7 comments
#687 - Remove the ultimate ancestor and split the grand MRCA
Pull Request -
State: closed - Opened by hyanwong about 2 years ago
- 23 comments
#683 - Raise warning when zero inference sites provided.
Issue -
State: closed - Opened by evolgenomics about 2 years ago
- 12 comments
#675 - Initial extend
Pull Request -
State: closed - Opened by jeromekelleher about 2 years ago
- 4 comments
#652 - Use imputation accuracy to determine the correct mismatch ratios
Issue -
State: open - Opened by hyanwong over 2 years ago
- 9 comments
#650 - Change metadata schema setters and getters in SampleData files to match tskit
Issue -
State: open - Opened by hyanwong over 2 years ago
- 1 comment
#608 - Possible (minor) bug in PC ancestors?
Issue -
State: open - Opened by hyanwong over 2 years ago
- 3 comments
#604 - Add ability to indicate that an ancestor is a sample
Issue -
State: open - Opened by hyanwong over 2 years ago
- 3 comments
#577 - Add recombination rate & tsdate link to the "real data" tute
Issue -
State: open - Opened by hyanwong almost 3 years ago
- 1 comment
#486 - Use dependency levels rather than epochs
Pull Request -
State: closed - Opened by hyanwong over 3 years ago
- 12 comments
#437 - Fix HMM for > 2 alleles
Issue -
State: open - Opened by jeromekelleher over 3 years ago
- 3 comments
#434 - Documentation for metadata schemas
Issue -
State: open - Opened by jeromekelleher over 3 years ago
Labels: enhancement
#429 - Flag up whether a mutation was placed because of a mismatch rather than because of shared ancestry
Issue -
State: open - Opened by hyanwong over 3 years ago
- 3 comments
#425 - Identifying Error from tsinfer Trees
Issue -
State: open - Opened by awohns over 3 years ago
- 3 comments
#422 - Output which haplotype fails
Pull Request -
State: closed - Opened by hyanwong over 3 years ago
- 12 comments
#419 - Output the haplotype being matched when find_path fails
Issue -
State: open - Opened by hyanwong over 3 years ago
- 2 comments