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Converting HaploBlocker to use NodeTraversals #26

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josiahseaman opened this issue Aug 26, 2019 · 0 comments
Open
4 tasks

Converting HaploBlocker to use NodeTraversals #26

josiahseaman opened this issue Aug 26, 2019 · 0 comments
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Currently, we have a working Database that supports ZoomLevels and we have a HaploBlocker algorithm that could produce ZoomLevels. However, the HaploBlocker implementation doesn't use the same objects and it hasn't been tested on non-linear graphs yet.

  • Object references changed
  • Object construction updated to NodeTraversal.objects.create()
  • Iterating over "all nodes" handled in a reasonable consistent order
  • Testing for non-linear test cases where summarization could trip over itself.
@josiahseaman josiahseaman added the enhancement New feature or request label Aug 26, 2019
@josiahseaman josiahseaman self-assigned this Aug 26, 2019
josiahseaman added a commit that referenced this issue Aug 26, 2019
@josiahseaman
#26 Simple_merge converted by copying the entire GraphGenome, Paths, …
bc49253 
…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.
josiahseaman added a commit that referenced this issue Aug 27, 2019
@josiahseaman
#26 Simple_merge test cases improved. internal_build_individuals() is…
59c18fd 
… working.
josiahseaman added a commit that referenced this issue Sep 3, 2019
@josiahseaman
#26 Split_one_group() updated for Database but Path - NodeTraversal -…
2fba2d8 
… ZoomLevel relationship is over complicated.
josiahseaman added a commit that referenced this issue Sep 3, 2019
@josiahseaman
#26 Split_groups Working fully. ZoomLevels are full copies of NodeTra…
96df52a 
…versal, which need not be contiguous.
josiahseaman added a commit that referenced this issue Sep 3, 2019
@josiahseaman
#26 Fix for Graph copying operation. Still hitting "too many SQL vari…
5159eae 
…ables".
josiahseaman added a commit that referenced this issue Sep 3, 2019
@josiahseaman
#26 changes to the DB schema for ZoomLevels being directly linked wit…
90570c4 
…h full copies of all Nodes and Paths. Data sharing removed.
josiahseaman added a commit that referenced this issue Sep 4, 2019
@josiahseaman
#26 Added xrange iterators
eba726d
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