Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / ANGSD/angsd issues and pull requests
#590 - Makefile: specify version.h as a dependency of all object files
Pull Request -
State: open - Opened by trofi about 1 year ago
#589 - Determine missingness by sample from a beagle file or binary glf file generated by angsd?
Issue -
State: open - Opened by BKrek89 about 1 year ago
#588 - Association test stops after chromosome 1
Issue -
State: open - Opened by Erikacj over 1 year ago
- 1 comment
#587 - Help with glf file - corrupt?
Issue -
State: open - Opened by Erikacj over 1 year ago
- 3 comments
#586 - [fix] Add howOften value check, add disable option
Pull Request -
State: closed - Opened by isinaltinkaya over 1 year ago
#585 - ANGSD stuck while processing vcf file subset
Issue -
State: open - Opened by ThibauldMichel over 1 year ago
#584 - realSFS is OOM killed
Issue -
State: closed - Opened by billiemaguire over 1 year ago
#583 - Angsd gets stuck in the same genomic region in independent runs
Issue -
State: open - Opened by hyperoplus over 1 year ago
#582 - Transitions not removed by -noTrans
Issue -
State: open - Opened by OKersten over 1 year ago
#581 - empty output files
Issue -
State: open - Opened by Sven-Winter over 1 year ago
- 22 comments
#580 - Inbreeding, HWE and SFS for heterozygosity
Issue -
State: open - Opened by irbinveliz over 1 year ago
- 1 comment
#579 - Filtering for LD with -sites
Issue -
State: open - Opened by RachelxGray over 1 year ago
#578 - What is PPmaf?
Issue -
State: open - Opened by shirasegoby over 1 year ago
#577 - [fix] Add missing parenthesis to assert macro
Pull Request -
State: closed - Opened by isinaltinkaya over 1 year ago
#576 - Generating beagle or saf files from text glf input (`-glf10_text`) fails when contig names contain underscores.
Issue -
State: open - Opened by zjnolen over 1 year ago
#575 - cannot convert vcf file to beagle binary format using the -vcf-gl option
Issue -
State: open - Opened by marce-sarrias over 1 year ago
- 3 comments
#574 - Calculate phenotypic variance explained by SNPs with GWAS output
Issue -
State: open - Opened by andreaestandia over 1 year ago
#573 - [build] Remove install -D to support osx build
Pull Request -
State: closed - Opened by isinaltinkaya over 1 year ago
#572 - Genotype file does not contain missing data
Issue -
State: open - Opened by dmacguigan over 1 year ago
#571 - Number of sites for SFS, incl. multi-allelic ones
Issue -
State: open - Opened by CIWa over 1 year ago
#570 - PROBS at positions
Issue -
State: open - Opened by lagoonas over 1 year ago
#569 - [fix] Add VCF spanning deletion check
Pull Request -
State: closed - Opened by isinaltinkaya over 1 year ago
#568 - visualization 2DSFS. plot2DSFS.R
Issue -
State: open - Opened by yangwukaidi over 1 year ago
- 2 comments
#567 - visualizing the 2D-SFS
Issue -
State: closed - Opened by yangwukaidi over 1 year ago
- 1 comment
#566 - Individual missingness and missing data
Issue -
State: open - Opened by jmhallas over 1 year ago
- 4 comments
#565 - Missing SNPS in doThetas Calculation
Issue -
State: open - Opened by tsehein over 1 year ago
#564 - Find older version ANGSD0.922 from commit#
Issue -
State: open - Opened by wul88 over 1 year ago
- 2 comments
#563 - Installing ANGSD on M1x ventura 13.2
Issue -
State: open - Opened by DaniEstevezBarcia over 1 year ago
#562 - [fix][VCF,indel] Add check for deletion in alleles
Pull Request -
State: closed - Opened by isinaltinkaya over 1 year ago
#561 - 4D SFS segmentation fault
Issue -
State: open - Opened by carolindahms over 1 year ago
- 7 comments
#560 - cleaner error if no SNP sites
Pull Request -
State: closed - Opened by abigailramsoe over 1 year ago
#559 - [bug?] Angsd sets qual of first site to 0
Issue -
State: open - Opened by isinaltinkaya over 1 year ago
#558 - Problem with -doThetas
Issue -
State: open - Opened by MehrabChowdhury1 over 1 year ago
- 3 comments
#557 - Error message 'Segmentation fault'
Issue -
State: closed - Opened by ThibauldMichel over 1 year ago
- 2 comments
#556 - Discrete covariates in -doAsso
Issue -
State: open - Opened by maehrlich1 over 1 year ago
#555 - Thetas per population/genomic clusters, summarizing across chromosomes
Issue -
State: open - Opened by akimmitt over 1 year ago
#554 - Segmentation fault in msHOT2glf
Issue -
State: open - Opened by niki3502 over 1 year ago
#553 - [bug?] Angsd fills GL tags of sites with missing GLs with 0s
Issue -
State: open - Opened by isinaltinkaya over 1 year ago
- 1 comment
#552 - ABBA-BABA_chimpHg19.fa.fai' looks older than corresponding fastafile
Issue -
State: open - Opened by cyadrogarcia almost 2 years ago
#551 - Failed to open .bam file error
Issue -
State: closed - Opened by staceyg947 almost 2 years ago
- 5 comments
#550 - Killed
Issue -
State: open - Opened by iremdnzl almost 2 years ago
- 1 comment
#549 - Is it possible to get population allele frequencies from PL values?
Issue -
State: open - Opened by marcoesca almost 2 years ago
#548 - Calculating Fst for windows with a fixed number of SNPs
Issue -
State: open - Opened by EmilyPhelps almost 2 years ago
- 1 comment
#547 - Permission denied after install
Issue -
State: open - Opened by Otorongo1 almost 2 years ago
- 3 comments
#546 - Merging beagle files
Issue -
State: closed - Opened by ghost almost 2 years ago
- 2 comments
#545 - How to calculate allele frequencies from genotype likelihood (beagle file format)
Issue -
State: open - Opened by Silvia-lme almost 2 years ago
#544 - Issue with multi-threaded BCF input for SAF
Issue -
State: open - Opened by malthesr almost 2 years ago
#543 - Is it possible to use a beagle input file to calculate HWE with ANGSD?
Issue -
State: open - Opened by beausoleilmo almost 2 years ago
#542 - No data for chromoId=0 chromoname=... with -doFasta
Issue -
State: open - Opened by beausoleilmo almost 2 years ago
#541 - Mystery positions in GWAS
Issue -
State: closed - Opened by EmilyPhelps almost 2 years ago
#540 - How to calculate the Global Population Branch Statistics (PBS) from per site PBS values
Issue -
State: open - Opened by wul88 almost 2 years ago
- 1 comment
#539 - [fix] Add -D__STDC_FORMAT_MACROS to FLAGS for C99
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#538 - realSFS - homozygous for the alternative allele returns a zero value.
Issue -
State: open - Opened by jcchacond about 2 years ago
- 3 comments
#537 - The reference or equations of Fst and theta pi
Issue -
State: closed - Opened by jiangzy26 about 2 years ago
#536 - Calculate PBS values based on more than three populations
Issue -
State: closed - Opened by jiangzy26 about 2 years ago
#535 - Compile problem at vcfReader
Issue -
State: closed - Opened by dithiii about 2 years ago
- 1 comment
#534 - Wrong header in realSFS fst index
Issue -
State: open - Opened by beausoleilmo about 2 years ago
- 4 comments
#533 - [fix]: Fix assert bug related to DNDEBUG flags #527
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#532 - [chore] Merge master to branch
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#531 - [fix]: Replace assert statements with aio assert
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#530 - RealSFS Watterson's Theta, Issue with size of dimension
Issue -
State: open - Opened by Raksha-95 about 2 years ago
- 1 comment
#529 - Heterozygosity/genotype calling alternative allele frequencies
Issue -
State: open - Opened by Mvwestbury about 2 years ago
- 3 comments
#528 - [fix] Fix compiler flags related sites parsing issue, fixes #527
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
- 4 comments
#527 - [bug report] angsd sites breaks due to compiler flags
Issue -
State: closed - Opened by isinaltinkaya about 2 years ago
- 1 comment
#526 - Merge develop
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#525 - Trying to run doAsso but receiving "Segmentation fault"
Issue -
State: open - Opened by beausoleilmo about 2 years ago
- 6 comments
#524 - Installation Error ::::: v0.938.
Issue -
State: closed - Opened by g-pacheco about 2 years ago
- 4 comments
#523 - Folded 2d SFS plot displays values beyond n1xn2 range
Issue -
State: open - Opened by wul88 about 2 years ago
- 9 comments
#522 - Estimating genotype likelihoods assuming inbreeding coefficient of 1
Issue -
State: open - Opened by phillipsar2 about 2 years ago
#521 - Run restart + data conversion
Issue -
State: closed - Opened by Imogen-D about 2 years ago
- 2 comments
#520 - Empty Files: `counts.gz` and `pos.gz` ::::: v0.935 || v0.939
Issue -
State: closed - Opened by g-pacheco about 2 years ago
- 9 comments
#519 - Tajimas D calculation for site windows
Issue -
State: closed - Opened by aguilar-gomez about 2 years ago
- 2 comments
#518 - Fetch upstream
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#517 - -dobcf --ignore-RG flag
Issue -
State: closed - Opened by ghost about 2 years ago
- 1 comment
#516 - bgzf_flush
Issue -
State: closed - Opened by pierrespc about 2 years ago
- 1 comment
#515 - angsd call snp vs gatk call snp
Issue -
State: closed - Opened by aaannaw about 2 years ago
- 1 comment
#514 - Fst value strongly affected by very low sample size, even with Bhatia -whichFst 1 option
Issue -
State: open - Opened by TeresaPegan about 2 years ago
- 3 comments
#513 - Subsets of geno files
Issue -
State: open - Opened by axelwilhelm about 2 years ago
- 4 comments
#512 - abbababa2 sample size discrepancy
Issue -
State: open - Opened by OliverPStuart about 2 years ago
#511 - [chore] Set crypto_try g++ to cxx; redirect output to /dev/null
Pull Request -
State: closed - Opened by isinaltinkaya about 2 years ago
#510 - realSFS command not found
Issue -
State: closed - Opened by shailij246 over 2 years ago
- 2 comments
#509 - File list reader needs to check for carriage returns in the file contents.
Issue -
State: closed - Opened by daviesrob over 2 years ago
- 1 comment
#508 - [feat,make] Add detect if -lcrypto is available on the system
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#507 - [fixtest] Fix printing log to logfile in testBeagleReader
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#506 - [fix,test] Fix printing log to logfile in testBeagleReader
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#505 - [fix] Add -f to rm to fix error 1 in tests caused by rm exit 1
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#504 - Overstimation of memory requirements
Issue -
State: closed - Opened by OliverPStuart over 2 years ago
- 2 comments
#503 - Installation issues
Issue -
State: closed - Opened by williamamarsh over 2 years ago
- 5 comments
#501 - Why max thread cap?
Issue -
State: open - Opened by OliverPStuart over 2 years ago
- 2 comments
#500 - [fix] unlogged banded SAF output in -doSaf 4 (beagle input); fix conflict
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#499 - assoc5 Issue with weights being nan or inf
Issue -
State: open - Opened by katcatalano over 2 years ago
- 3 comments
#498 - [fixleak]: Fix memory leaks in beagleReader
Pull Request -
State: closed - Opened by isinaltinkaya over 2 years ago
#486 - How do you unflatten a 2dSFS? Is Pop1 nrows or ncols in the matrix?
Issue -
State: closed - Opened by TeresaPegan over 2 years ago
- 8 comments
#480 - different number of loci for different runs with same script
Issue -
State: closed - Opened by shri1984 over 2 years ago
- 2 comments
#478 - error: ‘HTSCODECS_VERSION_TEXT’ undeclared
Issue -
State: closed - Opened by diegohernansanchez over 2 years ago
- 6 comments
#475 - Estimation of inbreeding coefficient by population
Issue -
State: open - Opened by jbruxaux over 2 years ago
- 4 comments
#474 - Why am I getting "Total number of sites analyzed: 0"?
Issue -
State: open - Opened by jingliulj over 2 years ago
- 8 comments
#466 - Issues with angsd -sites function
Issue -
State: closed - Opened by williamamarsh over 2 years ago
- 4 comments
#460 - Make an official conda version
Issue -
State: closed - Opened by ANGSD over 2 years ago
- 2 comments
#447 - duplicate sites in maf output
Issue -
State: closed - Opened by bishopia almost 3 years ago
- 8 comments