Ecosyste.ms: Issues

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GitHub / tskit-dev/msprime issues and pull requests

#2098 - simulating genome-wide SNPs

Issue - State: closed - Opened by mandresapata over 2 years ago - 3 comments

#2095 - Docs: add warning to not install to conda root

Issue - State: closed - Opened by jeromekelleher over 2 years ago
Labels: documentation

#2094 - Small update to error message for MSP_ERR_TIME_TRAVEL

Pull Request - State: closed - Opened by gtsambos over 2 years ago - 5 comments

#2092 - flake8 line length recs from Black have changed-- update this?

Issue - State: closed - Opened by andrewkern over 2 years ago - 4 comments
Labels: Infrastructure and tools

#2091 - Issue importing msprime into Python

Issue - State: closed - Opened by asadrh8 over 2 years ago - 9 comments

#2090 - Use new logo

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

#2086 - Change microsat default for lo to 1

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 1 comment

#2085 - Microsat verify

Pull Request - State: closed - Opened by andrewkern over 2 years ago - 4 comments

#2084 - Rework sectioning in mutations page

Issue - State: open - Opened by jeromekelleher over 2 years ago
Labels: documentation

#2083 - Docs for simulating multiple chromosomes with pedigrees

Pull Request - State: closed - Opened by apragsdale over 2 years ago - 3 comments

#2082 - Update docs on simulating multiple chromosomes

Issue - State: closed - Opened by apragsdale over 2 years ago - 1 comment

#2080 - clean up of microsatellite documentation and defaults

Pull Request - State: closed - Opened by andrewkern over 2 years ago - 3 comments

#2079 - Review interface and documentation.

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

#2078 - Justify default values for lo and hi

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

#2077 - Documentation for EL2 contradicts signature

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 1 comment

#2076 - More details on defaults for EL2

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

#2075 - More details on defaults for TPM

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 5 comments

#2074 - Review and document default params for microsat models

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

#2073 - Validation of microsat mutation models

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 13 comments

#2071 - Microsatellite mutations models

Pull Request - State: closed - Opened by andrewkern over 2 years ago - 21 comments

#2061 - Update to tskit C API 1.0.0

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 8 comments

#2060 - Update to tskit C 1.0

Issue - State: closed - Opened by jeromekelleher over 2 years ago
Labels: Infrastructure and tools

#2048 - Fix non-MassMigration edge case in from_old_style()

Pull Request - State: closed - Opened by grahamgower almost 3 years ago - 1 comment

#2044 - Simulating sex chromosomes

Issue - State: open - Opened by LukeAndersonTrocme almost 3 years ago - 9 comments
Labels: help wanted, question

#2013 - adding microsatellite mutation models

Issue - State: closed - Opened by andrewkern almost 3 years ago - 13 comments

#1993 - Use ``ancestral_to`` field on segments instead of global lookup table.

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

#1967 - "Unfriendly" behavior in notebooks when bugs occur.

Issue - State: closed - Opened by molpopgen about 3 years ago - 1 comment

#1952 - Remove tests/data directory

Issue - State: closed - Opened by jeromekelleher about 3 years ago - 1 comment
Labels: Infrastructure and tools

#1946 - sim_mutations and garbage collection

Issue - State: closed - Opened by mufernando about 3 years ago - 26 comments
Labels: Performance

#1931 - Add special case for merging non-overlapping segments

Issue - State: closed - Opened by jeromekelleher about 3 years ago - 4 comments
Labels: Performance

#1862 - Add support for ``store_full_arg`` option to pedigree sims.

Issue - State: closed - Opened by jeromekelleher over 3 years ago - 3 comments
Labels: enhancement

#1855 - Support internal samples in simulation through pedigree

Issue - State: open - Opened by jeromekelleher over 3 years ago - 22 comments
Labels: enhancement

#1762 - GenicSelection model cannot complete a sweep with a neutral trajectory.

Issue - State: open - Opened by molpopgen over 3 years ago - 23 comments
Labels: bug

#1653 - Integration of Selfing and Dormancy

Issue - State: open - Opened by TPPSellinger almost 4 years ago - 9 comments
Labels: enhancement

#1651 - Msprime slow for long genomes

Issue - State: closed - Opened by jeromekelleher almost 4 years ago - 19 comments
Labels: Performance

#1485 - "Sandbox violation" with meson 0.57

Issue - State: closed - Opened by jeromekelleher almost 4 years ago - 4 comments
Labels: bug, Infrastructure and tools

#1346 - Read hapmap reworking

Pull Request - State: closed - Opened by hyanwong about 4 years ago - 7 comments

#1299 - Docs for simulating with multiple chromosomes

Pull Request - State: closed - Opened by apragsdale about 4 years ago - 26 comments

#1087 - Mutation model conditioned on specific ancestral sequence

Issue - State: open - Opened by jeromekelleher over 4 years ago - 1 comment

#1065 - implementation of AA models

Pull Request - State: closed - Opened by GertjanBisschop over 4 years ago - 14 comments

#1037 - Remove extra parameter in DemographicEvent.get_ll_representation

Issue - State: open - Opened by jeromekelleher over 4 years ago - 2 comments

#1032 - Compare msprime against seq-gen #1018

Pull Request - State: closed - Opened by GertjanBisschop over 4 years ago - 67 comments