Ecosyste.ms: Issues

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GitHub / pystatgen/sgkit issues and pull requests

#1107 - Gene-drop estimation of genotype probabilities

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

#1106 - PC-Relate and Bi-allelic sites

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

#1104 - Add `display_pedigree` method

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 4 comments
Labels: auto-merge

#1103 - Single sample vcf import

Issue - State: open - Opened by jisqaqov over 1 year ago - 4 comments

#1102 - Option to treat float64 as float32 in write_vcf

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

#1101 - Use contig_id and filter_id arrays instead of attributes in write_vcf

Issue - State: open - Opened by timothymillar over 1 year ago - 1 comment
Labels: bug

#1100 - Endelman-Jannink GRM

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 4 comments
Labels: auto-merge

#1099 - Comparing datasets - remapping alleles.

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

#1098 - Need help how to calculate pbs in genome by windows way

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

#1097 - Pedigree visualisation

Issue - State: closed - Opened by timothymillar over 1 year ago - 3 comments

#1094 - Tajima's D for cohorts uses segregating sites for entire dataset

Issue - State: closed - Opened by percyfal over 1 year ago - 3 comments

#1093 - Pedigree contribution

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 5 comments
Labels: auto-merge

#1092 - Use ruff for Python linting?

Issue - State: open - Opened by hammer over 1 year ago - 1 comment
Labels: process + tools

#1090 - `vcf_to_zarr` creates zero-sized first chunk which results in incorrect dtype.

Issue - State: open - Opened by benjeffery over 1 year ago - 8 comments
Labels: bug, upstream

#1089 - Build failure due to missing cyvcf2 packages on linux

Issue - State: closed - Opened by tomwhite over 1 year ago - 1 comment
Labels: upstream

#1088 - Use new `contig_id` array in GWAS tutorial

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 1 comment
Labels: documentation, auto-merge

#1087 - Add pedigree_sel method

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 1 comment
Labels: auto-merge

#1086 - Change `max_str_len` utility function to return a Python int rather than an array scalar

Pull Request - State: closed - Opened by tomwhite over 1 year ago
Labels: auto-merge

#1085 - Upstream tests failing with "AttributeError: 'int' object has no attribute 'item'"

Issue - State: closed - Opened by tomwhite over 1 year ago
Labels: upstream

#1084 - Subset the samples?

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

#1083 - Add experimental `vcf_to_parquet` function

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

#1082 - How to read plink data in practice!

Issue - State: open - Opened by K-zhangfengwei over 1 year ago - 4 comments

#1081 - Benchmarks have stopped working

Issue - State: open - Opened by tomwhite over 1 year ago - 1 comment
Labels: process + tools

#1080 - Test on Python 3.11

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 3 comments
Labels: auto-merge, upstream

#1079 - NumPy 1.24 fixes

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

#1078 - Add skipna option to genomic_relationship

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 2 comments
Labels: auto-merge

#1077 - Consider standardizing the API of pca and pc_relate

Issue - State: open - Opened by timothymillar over 1 year ago - 4 comments
Labels: question

#1076 - Add skipna option to `genomic_relationship`

Issue - State: closed - Opened by timothymillar over 1 year ago

#1075 - Update founder kinship API in pedigree_kinship #1061

Pull Request - State: closed - Opened by timothymillar over 1 year ago
Labels: auto-merge

#1073 - Make `zarr_array_sizes` run in parallel

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 1 comment
Labels: auto-merge

#1072 - Add tutorial on relationship matrices

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 14 comments
Labels: auto-merge

#1071 - Add dask cluster docs

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

#1070 - Generated name for INFO field 'id' clashes with 'variant_id' from fixed VCF fields

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 2 comments
Labels: auto-merge

#1069 - Fix handling of VCFs with no samples

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

#1068 - VCF with zero sample columns results in divide by zero error

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

#1067 - Division by zero error with clinvar vcf

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

#1066 - Release 0.7.0

Issue - State: closed - Opened by tomwhite over 1 year ago - 7 comments
Labels: process + tools

#1064 - Give hint for how to work around Number='.' error when reading VCF

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 1 comment
Labels: auto-merge

#1063 - Use Codecov GitHub action since the PyPi package has been removed

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 1 comment
Labels: process + tools, auto-merge, upstream

#1062 - Endelman-Jannink GRM

Issue - State: closed - Opened by timothymillar over 1 year ago

#1061 - Update `pedigree_kinship` API to match `hybrid_relationship`

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

#1060 - Fix GPU tests

Pull Request - State: closed - Opened by aktech over 1 year ago - 2 comments
Labels: auto-merge

#1058 - Remove contigs dataset attribute

Issue - State: open - Opened by tomwhite over 1 year ago
Labels: IO, data representation

#1057 - Copy contigs from attribute to array in `load_dataset`

Issue - State: open - Opened by tomwhite over 1 year ago
Labels: IO

#1056 - Add variant id to simulate dataset

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 12 comments
Labels: auto-merge

#1055 - Add extra comment about filters to write_vcf

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

#1054 - Store contig names in a `contig_id` array

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 2 comments
Labels: auto-merge

#1053 - Hybrid relationship methods

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 7 comments
Labels: auto-merge

#1052 - Add `read_vcf` convenience function

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 5 comments
Labels: auto-merge

#1051 - Tests should use process-based dask

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

#1050 - Add convert_call_to_index method

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 2 comments
Labels: auto-merge

#1049 - Fix read_bgen for multiprocess dask cluster

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

#1048 - Method to convert genotypes to index

Issue - State: closed - Opened by tomwhite over 1 year ago - 3 comments
Labels: core operations

#1047 - Add `plink_to_zarr` and `zarr_to_plink` convenience functions

Pull Request - State: closed - Opened by tomwhite over 1 year ago
Labels: auto-merge

#1046 - Add retain_temp_files

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

#1045 - Update pre-commit

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

#1044 - Add read_chunk_length

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 10 comments
Labels: auto-merge

#1043 - path 'variant_contig' contains an array

Issue - State: closed - Opened by barneyhill over 1 year ago - 17 comments

#1042 - `vcf_to_zarr_sequential` high memory usage with large sample counts.

Issue - State: closed - Opened by benjeffery over 1 year ago
Labels: enhancement, performance

#1041 - Fix Sphinx build for pydata-sphinx-theme 0.13.0

Pull Request - State: closed - Opened by tomwhite over 1 year ago
Labels: auto-merge

#1039 - Defer numba guvectorize compilation for aggregate functions

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 4 comments
Labels: auto-merge

#1038 - Exclude pydata-sphinx-theme 0.13.0 since the build isn't working with it

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

#1037 - Sphinx build is failing with extension error (pydata_sphinx_theme)

Issue - State: closed - Opened by tomwhite over 1 year ago - 3 comments
Labels: process + tools, upstream

#1035 - Store contig names in a `contig_id` array

Issue - State: closed - Opened by timothymillar over 1 year ago - 4 comments

#1034 - Split the concat_zarrs step to avoid very large dask task counts

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 10 comments
Labels: auto-merge

#1033 - Subsetting a pedigree dataset

Issue - State: closed - Opened by timothymillar over 1 year ago

#1031 - Validate arrays of indices via DataArray attrs

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

#1030 - Support mixed-ploidy genotypes in `display_genotypes`

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 3 comments
Labels: auto-merge

#1029 - Run upstream tests on python>=3.9, since xarray no longer supports 3.8

Pull Request - State: closed - Opened by tomwhite over 1 year ago
Labels: auto-merge

#1028 - Improve method `identity_by_state`

Pull Request - State: closed - Opened by timothymillar over 1 year ago - 1 comment
Labels: auto-merge

#1027 - Add skipna option to method `identity_by_state`

Issue - State: closed - Opened by timothymillar over 1 year ago

#1026 - Performance issue with `identity_by_state` on samples dimension

Issue - State: closed - Opened by timothymillar over 1 year ago
Labels: bug

#1025 - Document GRM estimation using mean imputation.

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

#1024 - Fix PCA example output due to upstream change

Pull Request - State: closed - Opened by tomwhite almost 2 years ago
Labels: auto-merge

#1023 - Support quantitative trait values in plink

Issue - State: open - Opened by tomwhite almost 2 years ago
Labels: IO

#1022 - Allow `simulate_genotype_call_dataset` to add phasing info

Pull Request - State: closed - Opened by tomwhite almost 2 years ago
Labels: auto-merge

#1021 - Generate VCF header when writing, if no header is explicitly supplied

Pull Request - State: closed - Opened by tomwhite almost 2 years ago - 7 comments
Labels: auto-merge

#1020 - Generate VCF header when writing VCF

Issue - State: closed - Opened by tomwhite almost 2 years ago - 2 comments
Labels: IO

#1019 - Use `sample_*` variables if present to populate plink family fields when writing

Pull Request - State: closed - Opened by tomwhite almost 2 years ago - 4 comments
Labels: auto-merge

#1018 - Add asv benchmark for `write_plink`

Pull Request - State: closed - Opened by tomwhite almost 2 years ago
Labels: auto-merge

#1017 - Allow user to specify coordinate as phenotype in `write_plink`

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

#1015 - Add `kwargs` to `load_dataset` to pass to xarray, matching `save_dataset`

Pull Request - State: closed - Opened by tomwhite almost 2 years ago
Labels: IO, auto-merge

#1014 - Write pedigree data to VCF

Issue - State: open - Opened by timothymillar almost 2 years ago
Labels: IO

#1013 - Read pedigree data from VCF

Issue - State: open - Opened by timothymillar almost 2 years ago - 1 comment
Labels: IO

#1012 - Document reading tabular pedigree formats into sgkit

Issue - State: open - Opened by timothymillar almost 2 years ago - 3 comments
Labels: documentation, IO

#1010 - Write family information in `write_plink`

Issue - State: open - Opened by tomwhite almost 2 years ago - 3 comments
Labels: IO

#1009 - Populate parent_id variable in `read_plink`

Issue - State: open - Opened by tomwhite almost 2 years ago - 2 comments
Labels: IO

#1008 - Make sample_id from plink reader unique

Issue - State: open - Opened by tomwhite almost 2 years ago - 4 comments
Labels: IO

#1007 - Capitalization of peoples names in method names etc.

Issue - State: open - Opened by timothymillar almost 2 years ago - 3 comments
Labels: question

#1006 - Unused alleles being `""` is confusing for downstream tools - consider `None`?

Issue - State: open - Opened by benjeffery almost 2 years ago - 12 comments

#1004 - Consistent naming for IO functions

Issue - State: closed - Opened by tomwhite almost 2 years ago - 2 comments
Labels: IO

#1003 - Output plink

Pull Request - State: closed - Opened by tomwhite almost 2 years ago - 5 comments
Labels: auto-merge

#1002 - Replace `genotype_count` with `variant_genotype_count`

Pull Request - State: closed - Opened by timothymillar almost 2 years ago - 10 comments
Labels: auto-merge

#993 - Hybrid relationship matrices

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

#984 - Release 0.6.0

Issue - State: closed - Opened by tomwhite almost 2 years ago - 9 comments