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Commits on Jun 25, 2025

• add Google's sparsehash lib requirement

  

  Amy Williams

  committed
  ff4b278

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Commits on Jul 21, 2024

• update genetio submodule

  

  Amy Williams

  committed
  0405231

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Commits on Jul 17, 2024

• UGFIXes and update comments

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  Amy Williams

  committed
  0ffe385

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Commits on May 22, 2024

• add documentation; bump version number

  

  Amy Williams

  committed
  46a750d

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• add genetio submodule

  

  Amy Williams

  committed
  cefb492

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Commits on May 20, 2024

• update to work with genetio in local directory

  

  Amy Williams

  committed
  001b5c5

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• rename command line argument and associated variables

  

  Amy Williams

  committed
  d32bf54

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Commits on Mar 11, 2024

• only force informative marker every >= forceInformSeparation

  

  Amy Williams

  committed
  3121bee

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Commits on Feb 1, 2024

• use list not tuple for P regions

  

  Amy Williams

  committed
  b886868

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Commits on Dec 6, 2023

• detect and avoid applying states that are equivalent to applied ones but have opposite parent assignments

  

  Amy Williams

  committed
  030887b

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Commits on Dec 5, 2023

• refactor / return P regions to caller

  

  Amy Williams

  committed
  da9322a

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• change argument names

  

  Amy Williams

  committed
  b2687d8

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Commits on Aug 31, 2023

• code to evaluate HAPI's performance

  

  Amy Williams

  committed
  cefe681

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Commits on Aug 16, 2023

• bump version number

  

  Amy Williams

  committed
  9d9cc85

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• separate logic for errors and numMarkersSinceNonHetPar counts from whether we're transitioning from a forced informative marker

  

  Amy Williams

  committed
  e5be97e

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• BUGFIX: corner case when leaving IVambigPar region to PI state with ambig recombination

  

  Amy Williams

  committed
  1179624

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• - don't force an informative marker (i.e., enter one hap trans state) when

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  Amy Williams

  committed
  da5c2e9

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• BUGFIX:

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  Amy Williams

  committed
  a28e15b

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• Store maxNumMarkersSince as an optimization

  Show description for 0b362cc
  

  Amy Williams

  committed
  0b362cc

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• BUGFIX: don't mark forced informative markers not on a state path as errors

  

  Amy Williams

  committed
  980ca19

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• minor BUGFIX: trans haps at current marker differ from later ones

  

  Amy Williams

  committed
  36acf50

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• BUGFIX: corner case when IVambigPar at PI markers

  

  Amy Williams

  committed
  9d687e5

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• fix up forced informative marker tracking/conditions

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  Amy Williams

  committed
  42cd794

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• allow multiple OHT penalties in any interval

  

  Amy Williams

  committed
  f0156ff

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• Penalize errors with >= 0.5 recombinations, not 0.6

  

  Amy Williams

  committed
  19a2d05

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• BUGFIX: make numMarkersSinceOneHetPar error tolerant: subtract 10 instead of reset

  

  Amy Williams

  committed
  f45f9f1

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• need larger class of <fakeOneHetPar> states to count as if they were PI

  

  Amy Williams

  committed
  c3bffc3

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Commits on Dec 21, 2022

• Create LICENSE

  williamslab

  authored
  0c8f5a6

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Commits on Jul 23, 2022

• bump version number

  

  Amy Williams

  committed
  32a414f

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• remove unused <oneHapTransThreshold>

  

  Amy Williams

  committed
  09f7577

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• lower default <bothParHetThreshold> to 75

  

  Amy Williams

  committed
  be4a1bc

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• BUGFIX: assign <homParGeno> just before returning when <forceInform>

  

  Amy Williams

  committed
  20f613c

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Commits on Jul 9, 2022

• Accumulate <numMarkersSinceOneHetPar> at uninformative one het par states

  

  Amy Williams

  committed
  1a9a55b

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Commits on Jul 6, 2022

• Some todos

  

  Amy Williams

  committed
  f1b864c

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• In one hap trans regions, place markers using CmdLineOpts::forceInformSeparation

  

  Amy Williams

  committed
  e1d0578

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