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
#275 - `--keep` does not handle IID-only files properly when the main dataset contains FIDs
Issue -
State: closed - Opened by dvg-p4 2 months ago
- 3 comments
#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
#269 - Problem with combining different samples into a single plink 1 file for later input
Issue -
State: closed - Opened by sbird1000 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
#266 - PLINK v1.9 `sprintf()` compilation warnings: Does a way to silence/fix them exist?
Issue -
State: open - Opened by VicBoss1984 5 months ago
- 3 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
#260 - Pgenlib 0.90.1 is not installable from PyPI with Python 3.12.2 on Mac aarch64
Issue -
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
#234 - [pgenlib] support for `int8_t` in `read_alleles` and `read_alleles_and_phasepresent`
Issue -
State: closed - Opened by aryarm over 1 year ago
- 8 comments
#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
#225 - Error: REF allele on line 1071 of --pgen-diff .pvar file conflicts with loaded REF allele
Issue -
State: closed - Opened by hsmith9002 about 2 years ago
- 1 comment
#224 - Clarification in `pgen_spec`: what bytes goes into "variant record length" in PGEN header?
Issue -
State: closed - Opened by biona001 about 2 years ago
- 2 comments
#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
#221 - Feature request: check for presence of e.g. --keep-fam file before converting to temporary psam/pvar/pgen
Issue -
State: closed - Opened by sahwa 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
#216 - [pgenlib] `phasepresent_out` buffer has too few columns in `read_alleles_and_phasepresent_list`
Issue -
State: closed - Opened by aryarm about 2 years ago
- 4 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
#195 - pgenlib: when reading a .pgen file, must each row in that table be an individual? Or a SNP?
Issue -
State: closed - Opened by richelbilderbeek about 3 years ago
- 2 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