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[Pruning] Refactor phasing#125

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shihabdider wants to merge 55 commits intomastermskilab-org/gGnome:masterfrom refactor_phasingmskilab-org/gGnome:refactor_phasingCopy head branch name to clipboard

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Commits

Commits on Apr 30, 2021

• cleanup

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  c1342d4

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• get rid of unused parameters

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  c7744ee

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Commits on May 1, 2021

• initial commit apps.R

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  a25e97e

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Commits on May 2, 2021

• initial commit gurobi wrapper

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  f582cd4

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Commits on May 3, 2021

• expose threads parameter

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  c136076

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• add gurobi option to balance

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  a9313a5

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• bug fix in setting up parameters

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  ce35a7d

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• UDKJF

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  c335155

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• remove Rcplex dependency

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• remove rcplex dependency

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Commits on May 10, 2021

• add telomeric annotation to loose ends

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  f1beeef

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Commits on May 17, 2021

• add flag to allow cnloh in phased balance

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Commits on May 24, 2021

• merge master

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  58cb510

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• merge marcin's latest in peel

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  d63c1a5

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• initial commit

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  ea54ad0

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• add working code for parental graph sim, add force flag to ALT edges in balance

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  0dcc42a

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Commits on May 25, 2021

• fix balance code for edge marginals

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  6406428

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• cleanup parental, expose fix.emarginal in simulate.hets

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  b72b967

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Commits on May 26, 2021

• merge master

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  8adcaa9

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• merge master

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  f341b2e

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Commits on May 27, 2021

• merge parental

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  f4f19a6

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Commits on Jun 15, 2021

• update comments

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  d0ec5a3

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• merge master

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  c7553c7

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Commits on Jun 24, 2021

• add basic code for cnloh to phased.binstats

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Commits on Jun 26, 2021

• fix bug in phased.binstats

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  8fa33e5

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• merge master

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  03acd1c

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Commits on Jul 1, 2021

• update phased.binstats and balance to penalize CNLOH and reduce false positives

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  be13559

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Commits on Jul 5, 2021

• update phased.postprocess to disjoin gGraph before compressing allelic balance nodes

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  7c356ad

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Commits on Jul 14, 2021

• cnloh detection update

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  be1d2f3

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• merge latest from master

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  2d2bd2f

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Commits on Jul 20, 2021

• fix no ALT edges CNLOH bug

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  d47a83d

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Commits on Jul 22, 2021

• merge master

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  7c3f94b

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• merge latest

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  901ce1b

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Commits on Jul 24, 2021

• merge master with marcin's latest

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  350c6c2

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Commits on Jul 26, 2021

• start new postprocessing fx

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  0122c0f

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• merge master

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  e6f5ed0

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• bug fixes in postprocess

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  ca02541

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Commits on Jul 29, 2021

• stash changes to apps.R

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  356b453

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Commits on Jul 30, 2021

• merge master

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  bca20a1

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• update amp, modify NA node marking in phased.postprocess

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  2a0583d

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Commits on Aug 4, 2021

• bug fix

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  ff49d3e

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Commits on Aug 11, 2021

• stash most recent for amps)

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Commits on Aug 13, 2021

• latest with pre-balance collapsed nodes

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  e216f0c

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Commits on Sep 1, 2021

• stash new balance

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  1ed8c74

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• merge master

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  beeaf1c

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• initial commit for phasing with haplotypes

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  d3ba43b

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Commits on Sep 13, 2021

• stash changes for phasing

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  63592c1

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Commits on Feb 10, 2022

• merge latest from master

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  b00cc86

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Commits on Mar 22, 2022

• update branch

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  e0e80de

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• remove some merge conflict symbols

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  bbc6ffd

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Commits on Apr 19, 2022

• add everything

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  a4e76e3

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Commits on Apr 21, 2022

• update binstats

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  858c3a6

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• fix bugs, initial working balance

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  b4e9620

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Commits on May 30, 2022

• check in changes for phasing

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• Update converters.R

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  authored and

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