genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-03-16	Add code generating the new genotype files	zsloan
	Also made a large number of other fixes that proved necessary during testing
2022-03-16	Generate JSON file for target genotypes	zsloan
	Also store parents/type metadata from source genofiles
2022-03-16	Fix the way target/source genofiles were being processed + some other changes	zsloan
	- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles - references to the app context are removed in favor of just taking input as arguments or environment variables - Updated example commands
2022-03-16	Add function for mapping strain to sample pos + begin creating ↵	zsloan
	generate_new_genofiles function
2022-03-16	Add function for getting strain name from sample name	zsloan

2022-03-16	Change EOL from CRLF to LF	zsloan

2022-03-16	Minor changes/bug fixes	zsloan
	- Removed some unused code - Strip marker genotype to avoid newline character at end - Convert zip to list for marker genotypes - Add typing to group_samples - Rename strain_genofile to source_genofile
2022-03-16	Add in-progress gen_ind_genofiles.py	zsloan
	gen_ind_genofiles.py is a command line script to generate genotype files for groups of individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input