tskit-dev/tsinfer issues and pull requests

#764 - sgkit: Use ancestral_allele_index

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

#763 - sgkit: Use sequence length from dataset

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

#762 - Add info logging during "extend" setup

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

#761 - Release traceback memory if gets > 2GiB

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

#760 - Remove the "virtual-root-like" ancestor requirement from L&S matching

Issue - State: open - Opened by hyanwong almost 2 years ago

#759 - Do not require ancestors tree sequence to define internal nodes as samples

Issue - State: open - Opened by hyanwong almost 2 years ago

#758 - Update CHANGELOG.md

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

#757 - Fix readme MIME for PyPI

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

#756 - 0.3.0 pypi upload failed

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 5 comments
Labels: bug

#755 - Update changelog for release

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

#754 - Add --keep-intermediates CLI option

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 10 comments

#753 - Allow msprime.RateMap or equivalent to be used in pip installs

Issue - State: open - Opened by hyanwong almost 2 years ago - 8 comments

#752 - Temporarily disable --recombination-map in cli

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

#751 - Windows install fails because of msprime

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 5 comments
Labels: bug

#748 - Minimum viable sgkit dataset

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 28 comments

#739 - Variant method to return actual states

Issue - State: open - Opened by hyanwong almost 2 years ago - 4 comments

#729 - Unify SampleData and AncestorsData file formats

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

#728 - SampleData frontend for sgkit/xarray dataset

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 4 comments

#707 - How to stop people getting confused when inspecting ancestors tree sequences?

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

#701 - Set individuals table metadata schema to permissive_json

Issue - State: open - Opened by hyanwong about 2 years ago - 2 comments

#699 - Document SampleData attributes

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

#696 - Allow sample data and ancestors files to store their time units

Issue - State: open - Opened by hyanwong about 2 years ago - 8 comments

#688 - Document numpy array accessors in the sample data files?

Issue - State: closed - Opened by hyanwong over 2 years ago - 7 comments

#687 - Remove the ultimate ancestor and split the grand MRCA

Pull Request - State: closed - Opened by hyanwong over 2 years ago - 23 comments

#683 - Raise warning when zero inference sites provided.

Issue - State: closed - Opened by evolgenomics over 2 years ago - 12 comments

#675 - Initial extend

Pull Request - State: closed - Opened by jeromekelleher over 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

#642 - Use struct for node metadata

Pull Request - State: closed - Opened by hyanwong over 2 years ago - 17 comments

#608 - Possible (minor) bug in PC ancestors?

Issue - State: open - Opened by hyanwong almost 3 years ago - 3 comments

#604 - Add ability to indicate that an ancestor is a sample

Issue - State: open - Opened by hyanwong almost 3 years ago - 3 comments

#577 - Add recombination rate & tsdate link to the "real data" tute

Issue - State: open - Opened by hyanwong about 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 almost 4 years ago - 3 comments

#434 - Documentation for metadata schemas

Issue - State: open - Opened by jeromekelleher almost 4 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 almost 4 years ago - 3 comments

#425 - Identifying Error from tsinfer Trees

Issue - State: open - Opened by awohns almost 4 years ago - 3 comments

#422 - Output which haplotype fails

Pull Request - State: closed - Opened by hyanwong almost 4 years ago - 12 comments

#419 - Output the haplotype being matched when find_path fails

Issue - State: open - Opened by hyanwong almost 4 years ago - 2 comments

#416 - Add tsinfer specific schema for node metadata.

Issue - State: closed - Opened by jeromekelleher almost 4 years ago - 8 comments

#400 - Dynamically set precision values

Issue - State: open - Opened by hyanwong almost 4 years ago - 1 comment

#376 - Segfault in multiple tests on OS X, Python 3.9

Issue - State: closed - Opened by hyanwong almost 4 years ago - 52 comments

#374 - Use parsimony algorithm to compress likelihoods

Issue - State: open - Opened by jeromekelleher almost 4 years ago - 1 comment
Labels: enhancement

#373 - Dask and sgkit integration (major release)

Issue - State: open - Opened by jeromekelleher almost 4 years ago - 5 comments

#341 - lmdb out of memory error on tutorial example

Issue - State: open - Opened by stsmall almost 4 years ago - 33 comments

#284 - Ancestors time-binning

Issue - State: closed - Opened by hyanwong about 4 years ago - 2 comments

#274 - Implement `tsinfer info` CLI option

Issue - State: open - Opened by hyanwong over 4 years ago - 3 comments

#270 - tsinfer qc script

Issue - State: open - Opened by awohns over 4 years ago - 7 comments

#269 - Root node in real-data inferred tree sequence has huge number of children

Issue - State: open - Opened by awohns over 4 years ago - 4 comments

#189 - Add augment_samples() functionality

Issue - State: open - Opened by hyanwong about 5 years ago - 7 comments

#181 - Allow some ancestral states to be unknown

Issue - State: closed - Opened by hyanwong about 5 years ago - 7 comments

#155 - Too many breakpoints even in simple cases

Issue - State: open - Opened by hyanwong over 5 years ago - 7 comments

#147 - Extra parallelization possibilities for match_ancestors?

Issue - State: closed - Opened by hyanwong over 5 years ago - 25 comments

#107 - Make dependence on 0/1 mutations in ancestors ts explicit or remove

Issue - State: closed - Opened by jeromekelleher about 6 years ago - 4 comments

#105 - Add --keep-intermediates option to ``infer`` command

Issue - State: closed - Opened by jeromekelleher about 6 years ago

GitHub / tskit-dev/tsinfer issues and pull requests