import `plink-ng` as a git dependency#16

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aryarm wants to merge 244 commits intomainfrom

dep/update-poetry

Commits on Jan 22, 2022

Simulation framework and classes
mlamkin7
committed

Commits on Jan 24, 2022

added GeneticMarker class
mlamkin7
committed

Commits on Jan 26, 2022

Completed Classes
mlamkin7
committed

Commits on Feb 8, 2022

Restructure of repo
mlamkin7
committed

Commits on Feb 9, 2022

Commits on Feb 13, 2022

Commits on Feb 14, 2022

initiating haptools readme pages

Melissa Gymrek
authored and
Melissa Gymrek
committed
fixing minor readme typos

Melissa Gymrek
authored and
Melissa Gymrek
committed
minor readme changes

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding simgenotypes readme

Melissa Gymrek
authored and
Melissa Gymrek
committed

Commits on Feb 15, 2022

Commits on Feb 27, 2022

Commits on Mar 1, 2022

removed snakemake
mlamkin7
committed

Commits on Mar 6, 2022

update poetry to v1.2
aryarm
committed

Commits on Mar 7, 2022

Commits on Mar 15, 2022

Merge pull request #17 from aryarm/admix-sim
gymreklab
authored
adding haplotype classes

Melissa Gymrek
authored and
Melissa Gymrek
committed

Commits on Mar 16, 2022

correct version of simgenotype
mlamkin7
committed
handle SNP haplotype finding in transform

Melissa Gymrek
authored and
Melissa Gymrek
committed
initial simulator code

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding simphenotype readme

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding simphenotype readme

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding simphenotype readme

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding simphenotype readme

Melissa Gymrek
authored and
Melissa Gymrek
committed

Commits on Apr 1, 2022

update dependencies in lock
aryarm
committed

Commits on Apr 2, 2022

Commits on Apr 8, 2022

remove header b/c it already appears in the README
aryarm
committed

Commits on Apr 9, 2022

support gz and bz2 file extensions (see #19)
aryarm
committed

Commits on Apr 10, 2022

fmt with black
aryarm
committed

Commits on Apr 13, 2022

Commits on Apr 14, 2022

VCF and HAP file examples
s041629
authored
copy variant module from happler
aryarm
committed
cleaning up karyogram code

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge branch 'karyogram' of https://github.com/gymrek-lab/haptools into karyogram

Melissa Gymrek
authored and
Melissa Gymrek
committed
Added specifying chromosome functionality to simulating genotypes.
mlamkin7
committed
DAT example files
s041629
authored
Merge pull request #29 from gymrek-lab/feat/vcf_output
mlamkin7
authored
Example DAT files
s041629
authored
Merge pull request #31 from gymrek-lab/karyogram
gymreklab
authored
cleaning up karyogram code

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge pull request #32 from gymrek-lab/karyogram
gymreklab
authored
Admixed individuals from the US
s041629
authored
start on work for haplotype parser
aryarm
committed
solving karyogram color issues when color not specified

Melissa Gymrek
authored and
Melissa Gymrek
committed
Fixed error with regex parsing of chromosomes
mlamkin7
committed
Merge pull request #34 from gymrek-lab/feat/vcf_output
mlamkin7
authored
adding centromeres

Melissa Gymrek
authored and
Melissa Gymrek
committed
cleaning up karyogram user interface

Melissa Gymrek
authored and
Melissa Gymrek
committed
cleaning up karyogram user interface

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge pull request #35 from gymrek-lab/karyogram
gymreklab
authored
catching user errors in karyogram

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge pull request #36 from gymrek-lab/karyogram
gymreklab
authored
fixing broken links in readme to docs that moved

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding karyogram docs page

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding karyogram docs page

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding test karyogram image

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding test karyogram image

Melissa Gymrek
authored and
Melissa Gymrek
committed
typos in karyogram docs

Melissa Gymrek
authored and
Melissa Gymrek
committed
typos in karyogram docs

Melissa Gymrek
authored and
Melissa Gymrek
committed
adding example breakpoints

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge pull request #37 from gymrek-lab/docs
gymreklab
authored

Commits on Apr 15, 2022

Fixed floating point error
mlamkin7
committed

Commits on Apr 17, 2022

continue implementing Haplotypes.read and Haplotypes.iterate methods
aryarm
committed

Commits on Apr 19, 2022

Commits on Apr 21, 2022

Commits on Apr 22, 2022

Commits on Apr 23, 2022

Commits on Apr 24, 2022

Commits on Apr 28, 2022

Commits on May 5, 2022

Commits on May 18, 2022

fix TypeError in sim_genotype._write_vcf
aryarm
committed

Commits on Jun 9, 2022

Commits on Jun 15, 2022

Completed output vcf
mlamkin7
committed

Commits on Jun 16, 2022

Completed Output VCF and one test case
mlamkin7
committed

Commits on Jun 17, 2022

Added validation to input files for sim genotype
mlamkin7
committed

Commits on Jun 27, 2022

Merge pull request #53 from gymrek-lab/feat/vcf_output
mlamkin7
authored

Commits on Jun 30, 2022

Commits on Jul 1, 2022

adding apoe haplotype example

Melissa Gymrek
authored and
Melissa Gymrek
committed
changing apoe4 to hg19

Melissa Gymrek
authored and
Melissa Gymrek
committed
updating apoe4 example in transform docs

Melissa Gymrek
authored and
Melissa Gymrek
committed
Merge pull request #61 from gymrek-lab/test-transform
gymreklab
authored