Code

CompareReferences tool #7930

Code

Merged

droazen merged 22 commits intomasterbroadinstitute/gatk:masterfrom oc_referencecomparator_6837broadinstitute/gatk:oc_referencecomparator_6837Copy head branch name to clipboardJul 21, 2022

+7,565

Commits

Commits on Jul 18, 2022

• initial version of reference comparator tool

  orlicohen

  committed
  92bc20a

• basic skeleton code

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  committed
  85bc87a

• basic output table implementation

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  4335f4f

• working on output table

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  aea17a5

• updates to mode 1 comparison

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  committed
  7869a86

• refactoring/cleaning up existing code and adding write to file output featute

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  committed
  41ce2f6

• table to file output and integration tests

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  committed
  fa26001

• checking in references and expected outputs, minor tweaks

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  committed
  2671b43

• added md5 calculation mode code and integration tests

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  8f74dd7

• added table query functionality

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  006ada6

• refactored TableEntry

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  b344c64

• prelim unit tests

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  b2507a1

• unit tests for query methods, initial table analysis

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  committed
  e3b1aac

• unit tests updated

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  ee0db1a

• initial table analysis, work in progress

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  6c00ada

• table analysis for exact match and diffs in sequence, sequence name, sequence present

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  233bc97

• superset/subset table analysis

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  9a5cf45

• finished table analysis and added documentation

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  437eb84

• update to subset/superset logic, added case to analyze table unit test

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  5c887a1

Commits on Jul 20, 2022

• responding to review comments

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  committed
  dc59744

• responding to review comments, refactored ReferenceSequenceTable construction

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  committed
  70ec346

Commits on Jul 21, 2022

• responding to final review comments

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  committed
  a736923