I've developed a more precise and refined forensic vocabulary since first working on this project, but vestiges of my original terminology remain. The purpose of this PR is to bring the profile JSON schema (and, where reasonable, variable names in code) up to date.
This branch touches a lot of files, but most of the changes are subtle. For instance, in the JSON files, the "allele" key was replaced with "haplotype", the "haplotype" key (referring to the haplotype of origin when inferred or known such as for simulated profiles) was replaced with "haploindex", and the "allele_counts" key was replaced with "typing_result". Similar changes were propagated in the Python API, the core modules, and code in the test suite.
Also, updated .gitattributes to correctly mark .ipynb files as documentation. Closes #108.
[x] Changes are clearly described above
[x] Any relevant issue threads are referenced in the description
[x] Any new features are tested (see docs/DEVEL.md for details)
I've developed a more precise and refined forensic vocabulary since first working on this project, but vestiges of my original terminology remain. The purpose of this PR is to bring the profile JSON schema (and, where reasonable, variable names in code) up to date.
This branch touches a lot of files, but most of the changes are subtle. For instance, in the JSON files, the "allele" key was replaced with "haplotype", the "haplotype" key (referring to the haplotype of origin when inferred or known such as for simulated profiles) was replaced with "haploindex", and the "allele_counts" key was replaced with "typing_result". Similar changes were propagated in the Python API, the core modules, and code in the test suite.
Also, updated
.gitattributesto correctly mark.ipynbfiles as documentation. Closes #108.