pyhegp/tests/helpers, branch main Homomorphic encryption of genotypes and phenotypes http://git.systemreboot.net/pyhegp/atom?h=main 2026-01-28T01:18:09+00:00 Require that (chromosome, position) in genotype frames is unique. 2026-01-28T01:18:09+00:00 Arun Isaac 2026-01-28T01:04:40+00:00 urn:sha1:83fff7bec63b80e5c89bbffbac95504660013dce Earlier, we required that (chromosome, position, reference) was unique. We tighten this restriction requiring (chromosome, position) be unique. Therefore, there can be only one reference allele at any given chromosome and position. Restrict reference to single character. 2026-01-28T01:18:09+00:00 Arun Isaac 2026-01-28T01:00:44+00:00 urn:sha1:d4afd6d2a02c12697c959c046cd345ab0a645f72 Add intercept column in phenotypes file. 2026-01-16T23:06:32+00:00 Arun Isaac 2026-01-14T20:29:33+00:00 urn:sha1:a76dedb432aa99f53681144c488ac19b9c23e660 Generate unique SNPs in genotype frames without dropping duplicates. 2025-09-05T19:15:12+00:00 Arun Isaac 2025-09-05T19:15:12+00:00 urn:sha1:773548d24fbbd3dd13a96c00c1a50f97fecdf8b8 Earlier, we were generating unique SNPs in genotype frames by dropping duplicates. This meant we couldn't control the number of SNPs. Rejection sampling is also not an option because it is too expensive. So, we now generate unique SNPs directly, by first generating a list with unique elements and then converting to a data frame. Deduplicate genotype frame metadata generation. 2025-09-05T15:11:19+00:00 Arun Isaac 2025-09-05T15:11:19+00:00 urn:sha1:f34d90f5b8ef80aceef22a0e544d738f468b0739 Abstract out generation of genotype frame metadata (namely chromosome, position and reference) from summaries and genotype_frames into a new helper function genotype_metadata. Limit values in genotype and phenotype strategies. 2025-09-04T21:05:31+00:00 Arun Isaac 2025-09-04T21:05:31+00:00 urn:sha1:09da0ae07115600010f267d3c5bd164e7cd786e2 Parameterize number of samples in phenotype frame strategy. 2025-09-04T21:04:18+00:00 Arun Isaac 2025-09-04T20:15:22+00:00 urn:sha1:c25159e08193779809eec63418f22679be052581 Parameterize number of samples in genotype frame strategy. 2025-09-04T19:57:16+00:00 Arun Isaac 2025-09-04T19:56:51+00:00 urn:sha1:e4ea95ccc95da090f9aabd55b617f7fb5234ae30 Parameterize presence of reference column in genotype frame strategy. 2025-09-04T19:55:33+00:00 Arun Isaac 2025-09-04T19:55:33+00:00 urn:sha1:afca032af0a70b98457ef03f7c218efe2c8d417c Add keys strategy. 2025-09-04T19:42:47+00:00 Arun Isaac 2025-09-04T19:42:47+00:00 urn:sha1:5b97a40f493dfd250831d303f5e3e4ba0a8a2c08 Add keys strategy, and use it.