Code

functions for meta analysis#76

Code

Open

mconomos wants to merge 22 commits intodevelUW-GAC/GENESIS:develfrom metaUW-GAC/GENESIS:metaCopy head branch name to clipboard

+424-20

Commits

Commits on Oct 1, 2021

• initial commit for meta analysis functions

  

  mconomos

  authored and

  mconomos

  committed
  4f7e506

  Copy full SHA for 4f7e506

• wip

  

  mconomos

  authored and

  mconomos

  committed
  4a0d43e

  Copy full SHA for 4a0d43e

Commits on Oct 2, 2021

• drop duplicate rows when not returning score.cov

  

  mconomos

  authored and

  mconomos

  committed
  fc76382

  Copy full SHA for fc76382

• fix typo

  

  mconomos

  authored and

  mconomos

  committed
  1f0cf47

  Copy full SHA for 1f0cf47

• fix arguments to method

  

  mconomos

  authored and

  mconomos

  committed
  84e3a22

  Copy full SHA for 84e3a22

Commits on Oct 6, 2021

• pack symmetric matrix to save memory

  smgogarten

  committed
  46af7f9

  Copy full SHA for 46af7f9

• add unit test for meta prep

  smgogarten

  committed
  0f31067

  Copy full SHA for 0f31067

Commits on Oct 7, 2021

• score.cov is returned only for aggregate iterators

  Show description for 5bd09a3
  smgogarten

  committed
  5bd09a3

  Copy full SHA for 5bd09a3

• unit tests for meta

  smgogarten

  committed
  4688b70

  Copy full SHA for 4688b70

• remove some ids to reduce output size

  

  mconomos

  authored and

  mconomos

  committed
  117b9ce

  Copy full SHA for 117b9ce

• drop varid column for space

  

  mconomos

  authored and

  mconomos

  committed
  e813aa0

  Copy full SHA for e813aa0

Commits on Oct 8, 2021

• add AF.max argument; add effective MAC for imputed variants

  

  mconomos

  authored and

  mconomos

  committed
  120ff5b

  Copy full SHA for 120ff5b

• can't refer to GenotypeBlockIterator inside method for SeqVarIterator; will need separate method

  smgogarten

  committed
  285af47

  Copy full SHA for 285af47

• revise unit tests

  smgogarten

  committed
  3921427

  Copy full SHA for 3921427

• add option to return alleles in variantInfo for GenotypeData

  smgogarten

  committed
  a00bcf5

  Copy full SHA for a00bcf5

Commits on Oct 9, 2021

• add metaPrepScores method for GenotypeIterator object

  smgogarten

  committed
  e3e5803

  Copy full SHA for e3e5803

Commits on Oct 14, 2021

• confirm alleles are included in output with GenotypeData object

  smgogarten

  committed
  dce334c

  Copy full SHA for dce334c

• add support for SeqVarListIterator in metaPrepScores

  Show description for fdd43f1
  smgogarten

  committed
  fdd43f1

  Copy full SHA for fdd43f1

Commits on Oct 21, 2021

• add MAC.min and DS.min filters to .prepGenoBlock

  

  mconomos

  authored and

  mconomos

  committed
  83feba5

  Copy full SHA for 83feba5

• add missing argument

  

  mconomos

  authored and

  mconomos

  committed
  220bcad

  Copy full SHA for 220bcad

Commits on Oct 22, 2021

• fix parameter name

  

  mconomos

  authored and

  mconomos

  committed
  b76e681

  Copy full SHA for b76e681

Commits on Nov 30, 2021

• temporary fix to pack issue

  

  mconomos

  authored and

  mconomos

  committed
  5e6baf0

  Copy full SHA for 5e6baf0