This repository has been archived by the owner on Mar 20, 2020. It is now read-only.
I23 haplo conversion #27
Draft
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…. Getters for .specimens, .upstream, .downstream. Now comes the harder work of thinking through the algorithm in database terms.
…s can visit Nodes from any zoom layer. There is one path per accession per zoom layer. Paths and nodes contain links to their parent/child summaries.
…he code. But zoom filtering is becoming cumbersome.
…nvenience. WIP: Converting all tests and code to database queries. GraphTest now passing.
…hing the whole graph.
…derstand Profiles well enough to update generate_profiles(). This may be the same concept as Haploblocker identifying the set of unique signatures at a locus.
…and NodeTraversals to a new ZoomLevel. I'm committing here because I want to save a working test state. Using pycharm, make sure you use Django Tests (manage.py) with no Target. This will run all tests in the project. I added bulk_create for NodeTraversals because the KE_chromo test was ridiculously slow.
|
I will take a look at it :) |
… ZoomLevel relationship is over complicated.
…versal, which need not be contiguous.
…h full copies of all Nodes and Paths. Data sharing removed.
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adds in ZoomLevels so multiple Graphs can share the same Nodes and Paths. Each GraphGenome has many ZoomLevels. Each ZoomLevel is a complete Graph, summarizing the layer of zoom-1. Zoom 0 is nucleotide level. HaploBlocker algorithm is being converted to use these database objects.