Code

Hipstr flanking bp pos fix#147

Code

Merged

LiterallyUniqueLogin merged 24 commits intogymrek-lab:developgymrek-lab/TRTools:developfrom Kulivox:hipstr-flanking-bp-pos-fixKulivox/TRTools:hipstr-flanking-bp-pos-fixCopy head branch name to clipboardFeb 11, 2022

+246-85

Commits

Commits on Feb 2, 2022

• added new field to TRRecord which holds position of full alleles

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• HipSTR harmonization sets TRRecord position to position of record without flanking bp at the start

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Commits on Feb 3, 2022

• Added correct types to mergeutils.py functions

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• Added multipledispatch lib to requirements

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• Fixed problems revealed by static type analysis and added functions that use multiple dispatch

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  786bfee

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• Fixed bug in compareSTR.py

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• Added utility function to tr_harmonizer.py

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• Implemented improved record comparison, records are now harmonized before the ability to compare them is calculated, fixes HipSTR issue

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• updated RELEASE_NOTES.rst

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Commits on Feb 4, 2022

• added utility function to mergeutils.py

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Commits on Feb 5, 2022

• Removed multiple dispatch and created new function for choosing which harmonized record should be skipped

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Commits on Feb 6, 2022

• added tests for additions to TRHarmonizer

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• removed duplicated function in mergeutils.py

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• added test for getMinHarmonizedRecords from mergeutils

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• updated compareSTR.py to use harmonized values UpdateComparisonResults

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• added tests for comparison of harmonized HipSTR records

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Commits on Feb 7, 2022

• removed incomplete test

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• added docstring for new function in mergeutils.py

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• Updated release notes to better describe changes

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Commits on Feb 8, 2022

• Update docs, remove extra copies of VCFs

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• More doc cleanup

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Commits on Feb 9, 2022

• added new test cases to test_mergeutils.py

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• Added new test cases to test_compareSTR.py

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Commits on Feb 11, 2022

• removed HarmonizeRecords function, reordered conditions in main loop of compareSTR.py to correctly handle None Records from getNextRecords

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