Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / chrchang/plink-ng issues and pull requests

#276 - `--update-sex` does not assume FID to be 0 like `--keep`

Issue - State: closed - Opened by BinglanLi 2 months ago - 1 comment

#274 - PLINK 1.9: Issues with --make-bed and empty .fam file

Issue - State: closed - Opened by GGarrido013 3 months ago - 1 comment

#273 - Error: Duplicate phenotype/covariate ID

Issue - State: closed - Opened by AnjeGrobler 3 months ago - 1 comment

#272 - Adapt CI/CD for python `pgenlib` to test against numpy 2.0

Pull Request - State: closed - Opened by aryarm 4 months ago - 5 comments

#271 - clumping

Issue - State: closed - Opened by zkhamis 4 months ago

#270 - --homozyg-group question

Issue - State: closed - Opened by ocdorsey 4 months ago - 1 comment

#268 - pgenlibr: ReadList question

Issue - State: closed - Opened by gidiesse 4 months ago - 7 comments

#267 - Persistent download URLs for built binaries?

Issue - State: closed - Opened by espenhgn 4 months ago - 2 comments

#265 - Obtaining different results from the same data in different formats

Issue - State: closed - Opened by salcc 5 months ago - 2 comments

#264 - plink2 --update-name issue

Issue - State: closed - Opened by Yangyuqing0797 7 months ago - 1 comment

#263 - Logistic regression returns NAs output---FIRTH_CONVERGE_FAIL

Issue - State: closed - Opened by shenlan17 7 months ago - 1 comment

#262 - build: Add a Github Actions workflow that builds wheels on ARM64 Mac OS.

Pull Request - State: closed - Opened by pettyalex 7 months ago - 3 comments

#261 - fix: Include simde in Pgenlib python package, fixing aarch64 build

Pull Request - State: closed - Opened by pettyalex 7 months ago - 1 comment

#259 - can plink handle vcf files with * notation?

Issue - State: closed - Opened by elizakirsch0 8 months ago - 1 comment

#258 - Request for pgen files to include a version number in the header

Issue - State: open - Opened by cmnbroad 8 months ago - 8 comments

#257 - File read error when converting .vcf to PLINK .ped and .map file

Issue - State: closed - Opened by ryshi06 8 months ago - 1 comment

#256 - Can't run anny PLINK command on Ubuntu 22.04

Issue - State: closed - Opened by MatusBuci 8 months ago - 1 comment

#255 - Compilation failure

Issue - State: closed - Opened by danieller 8 months ago - 1 comment

#254 - Request: plink2 --extract/exclude-if-info [key(s)...]

Issue - State: open - Opened by kscott-1 8 months ago - 1 comment

#253 - how to install in arm64 ? thks

Issue - State: open - Opened by zsw-test 9 months ago - 4 comments

#252 - CentOs7.9 install plink1.9 error

Issue - State: open - Opened by gaozejie 9 months ago - 3 comments

#251 - Feature Request: Upstream Dockerfile

Issue - State: open - Opened by kscott-1 10 months ago

#250 - plink2 --sample-count running out of memory

Issue - State: closed - Opened by janxkoci 11 months ago - 5 comments

#249 - pgenlibr: multi-threading?

Issue - State: open - Opened by agilly-regn 12 months ago - 1 comment

#249 - pgenlibr: multi-threading?

Issue - State: open - Opened by agilly-regn 12 months ago - 1 comment

#248 - --score precision error

Issue - State: closed - Opened by smlmbrt about 1 year ago - 3 comments

#247 - 0 phenotype values present after --pheno.

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

#247 - 0 phenotype values present after --pheno.

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

#246 - Overly general "--bcf file could not be scanned twice"

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

#246 - Overly general "--bcf file could not be scanned twice"

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

#245 - Multithread-only --glm floating point exception

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

#245 - Multithread-only --glm floating point exception

Issue - State: open - Opened by chrchang about 1 year ago - 2 comments

#244 - CNV-SNP LD

Issue - State: closed - Opened by Qijie0615 about 1 year ago - 2 comments

#244 - CNV-SNP LD

Issue - State: closed - Opened by Qijie0615 about 1 year ago - 2 comments

#243 - Python API import errors with latest version

Issue - State: closed - Opened by francois-a over 1 year ago - 5 comments

#243 - Python API import errors with latest version

Issue - State: closed - Opened by francois-a over 1 year ago - 5 comments

#242 - Error: No entries in phenotype.txt correspond to loaded sample IDs.

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

#241 - A question about --a1-allele

Issue - State: closed - Opened by shenlan17 over 1 year ago - 1 comment

#241 - A question about --a1-allele

Issue - State: closed - Opened by shenlan17 over 1 year ago - 1 comment

#240 - Document mapping of chromosomes to numeric codes with --output-chr 26

Issue - State: closed - Opened by dvg-p4 over 1 year ago - 1 comment

#239 - Correctness in Ref/Alt when converting to VCF

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

#238 - Adding columns from VCF into plink result files

Issue - State: closed - Opened by pengxiao78 over 1 year ago - 1 comment

#237 - --score with mean imputation calculates allele frequency for unneeded alleles

Issue - State: closed - Opened by dvg-p4 over 1 year ago - 3 comments

#236 - Plink2 round-tripping vcf->pgen->vcf does not preserve contig names

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

#235 - V2.00a3.7 alpha.4

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

#233 - ERROR: compilation failed for package 'pgenlibr'

Issue - State: closed - Opened by xug3 over 1 year ago - 8 comments

#232 - `Error: Non-concatenating --pmerge[-list] is under development.`

Issue - State: open - Opened by jacorvar over 1 year ago - 9 comments

#231 - read haploid dosages with pgenlib

Issue - State: open - Opened by 23andme-jaredo over 1 year ago - 5 comments

#230 - Specifying pairs for IBD estimation

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

#229 - list `oldest-supported-numpy` as a build dependency

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

#228 - plans to get pgenlib on bioconda?

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

#227 - sysconf(_SC_NPROCESSORS_ONLN) should not be used

Issue - State: closed - Opened by jbd almost 2 years ago - 6 comments

#226 - problem about plink2

Issue - State: closed - Opened by Mia1037 almost 2 years ago - 1 comment

#223 - How to get 0x55 in pgen_spec?

Issue - State: closed - Opened by biona001 about 2 years ago - 2 comments

#222 - Update installation instructions for python

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

#220 - Error: .pgen file read failure: File appears to be corrupted.

Issue - State: closed - Opened by Hoeze about 2 years ago - 22 comments

#219 - Half-missing call in .ped file at variant 55, line 640.

Issue - State: closed - Opened by Daluser1 about 2 years ago - 1 comment

#218 - Mismatching allele code

Issue - State: closed - Opened by ys8358 about 2 years ago - 3 comments

#217 - [pgenlib] pip install fails with v0.81.2

Issue - State: closed - Opened by aryarm about 2 years ago - 7 comments

#215 - python setup.py incorrect path

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

#214 - Distance matrices meets multiallelic sites

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

#213 - Load imbalance in plink2_matrix_calc.cc::CalcGrmPartThread().

Issue - State: closed - Opened by LorienLV over 2 years ago - 6 comments

#212 - Add option to write out allele frequencies when running --glm in PLINK v2

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

#211 - plink1.9 --23file, chromosoem out of order

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

#210 - covariates in plink

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

#209 - id-paste=iid option for --export A-transpose

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

#208 - Fix Plink2 build on Apple Silicon MacOS: Call NEON SIMD instructions with constants.

Pull Request - State: closed - Opened by pettyalex over 2 years ago - 7 comments

#207 - Allow Plink 1.9 to compile & run on Apple Silicon

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

#206 - GitHub Actions checks if `pgenlib` can be installed

Pull Request - State: closed - Opened by richelbilderbeek over 2 years ago

#205 - pgen spec: when bottom 3 bits of the record type is 3

Issue - State: closed - Opened by kose-y over 2 years ago - 2 comments

#204 - Fail to install 'pgenlibr' R package

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

#203 - [Fix] clang does not support execute yet

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

#202 - [help] Vector/matrix encoding of alleles

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

#201 - Error: Failed to extract eigenvector(s) from GRM.

Issue - State: closed - Opened by ManuelMoradiellos almost 3 years ago - 5 comments

#200 - Heterozygous haploid errors

Issue - State: closed - Opened by klmartinez almost 3 years ago - 1 comment

#199 - failed to change

Issue - State: closed - Opened by biozzq almost 3 years ago

#198 - recommended use in C++ project

Issue - State: closed - Opened by jvanalstine almost 3 years ago - 6 comments

#197 - --clump in plink2

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

#196 - Wrong ordering in physical positions

Issue - State: closed - Opened by zillurbmb51 almost 3 years ago - 4 comments

#194 - Feature request: pgenlibr: save pgen R data to file

Issue - State: open - Opened by richelbilderbeek about 3 years ago - 2 comments

#193 - Plans to get pgenlibr on CRAN?

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

#192 - splitting by chromosomes produce different number of samples in each chromosome

Issue - State: closed - Opened by zillurbmb51 about 3 years ago - 8 comments

#191 - failed to open bed file

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

#190 - plink2 --within flag not clustering

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

#189 - "--cnv-freq-exclude-above" works the same with "--cnv-freq-include-exact"

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

#188 - Minor python Readme improvements

Pull Request - State: closed - Opened by lbergelson about 3 years ago

#187 - Disable calculation of allele frequencies?

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

#186 - Possible to encode a bed file with no variants?

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

#185 - error making .bed file using plink

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

#184 - plink2: Error: Unrecognized flaf (--pmerge-list)

Issue - State: closed - Opened by zillurbmb51 over 3 years ago - 1 comment