Code

Main logged - verbose + emission ABC#21

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michaelJwilson wants to merge 131 commits intomain_loggedmichaelJwilson/CalicoST:main_loggedfrom main_logged_verbose_abcmichaelJwilson/CalicoST:main_logged_verbose_abcCopy head branch name to clipboard

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Commits

Commits on Aug 12, 2024

• add logging and tidy for calicost_main

  

  Michael J. Wilson

  committed
  e5b3b45

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• add logging info for hmrf_concatenate_pipeline.

  

  Michael J. Wilson

  committed
  3009a32

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• add logging for hmrfmix_concatenate_pipeline

  

  Michael J. Wilson

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  dd8963b

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• add logging for hmm_NB_BB_nophasing

  

  Michael J. Wilson

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  12cef43

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• adding logging for update params in utils_hmm

  

  Michael J. Wilson

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  c932e83

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• add logging of hmm_NB_BB_nophasing_v2

  

  Michael J. Wilson

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  50246d2

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• add logging to hmm_NB_BB_phaseswitch

  

  Michael J. Wilson

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  a35d751

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• add logging to hmrf and utils_IO.

  

  Michael J. Wilson

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  221a089

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• add logging to hmrf_pipeline

  

  Michael J. Wilson

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  8d51750

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• add logging on Weighted_NegativeBinomial

  

  Michael J. Wilson

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  8ea8908

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• add logging of emission fitting.

  

  Michael J. Wilson

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  bd8280b

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• finish logging utils distribution fitting

  

  Michael J. Wilson

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  0707450

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• set error on MKL thread setting in calicost_supervised.

  

  Michael J. Wilson

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  e005dd6

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• fix == bug in setup.py

  

  Michael J. Wilson

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  61d0ea9

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• fix errors with configuration of inner and outer loops

  

  Michael J. Wilson

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  01a2d91

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• fix issues around string and bracks from additional logging.

  

  Michael J. Wilson

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  915e41d

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• fix errors around disp=False (statsmodels) and inconsistent conda/pip environment

  

  Michael J. Wilson

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  0e3e12a

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• fix issue with multiple loggers.

  

  Michael J. Wilson

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  e1e51fa

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• fix prefix bug

  

  Michael J. Wilson

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  c689eb1

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Commits on Aug 15, 2024

• revert imports & prefix checks.

  

  Michael J. Wilson

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  d5ebb3c

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• revert imports in calicost supervised.

  

  Michael J. Wilson

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  19926b3

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• revert import for hmm_nophasing

  

  Michael J. Wilson

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  cbca8c0

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• revert imports for hmm_NB_BB_nophasing_v2

  

  Michael J. Wilson

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  f669dab

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• revert imports for hmm phaseswitch

  

  Michael J. Wilson

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  bcf1b6d

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• revert imports for hmrf

  

  Michael J. Wilson

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  be5524f

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• revert imports for utils IO.

  

  Michael J. Wilson

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  6c17702

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• revert imports for utils hmm

  

  Michael J. Wilson

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  3b1d698

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• revert imports for distribution fitting.

  

  Michael J. Wilson

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  1c5a3e4

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• add utils hmm njit import

  

  Michael J. Wilson

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  3c594d5

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• fix calicost supervised imports.

  

  Michael J. Wilson

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  ffb2b9f

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• fix runtime logging.

  

  Michael J. Wilson

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  fc6f8b3

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• import bug

  

  Michael J. Wilson

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  32e2221

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• fix spelling mistake

  

  Michael J. Wilson

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  48ca56a

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• log comparative likelihoods.

  

  Michael J. Wilson

  committed
  ba4de3e

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• fix

  

  Michael J. Wilson

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  47d2b60

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• fix

  

  Michael J. Wilson

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  63be476

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Commits on Aug 16, 2024

• improve runtime logging

  

  Michael J. Wilson

  committed
  69f65c6

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• update utils hmm logging to show n spots.

  

  Michael J. Wilson

  committed
  805e475

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• fix logging error from multiple args

  

  Michael J. Wilson

  committed
  da84c58

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• fix typo in hmrf logging

  

  Michael J. Wilson

  committed
  b710837

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• update logging strings.

  

  Michael J. Wilson

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  a2c3644

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• logging edits

  

  Michael J. Wilson

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  8568d1a

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• log hmrfmix_reassignment_posterior_concatenate.

  

  Michael J. Wilson

  committed
  def222d

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• more logging improvements. remove deprecated code.

  

  Michael J. Wilson

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  ff59608

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• add use defaults statement

  

  Michael J. Wilson

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  6aaa621

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• edit logging for ARI and bb diff.

  

  Michael J. Wilson

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  a06c4e8

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• log neyman pearson.

  

  Michael J. Wilson

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  75765aa

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• improved logging.

  

  Michael J. Wilson

  committed
  47972d1

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• update logging.

  

  Michael J. Wilson

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  009734c

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• update logging

  

  Michael J. Wilson

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  aa15da1

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• improve logging

  

  Michael J. Wilson

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  00427d3

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• improved logging

  

  Michael J. Wilson

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  e049c95

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• fix logging

  

  Michael J. Wilson

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  6cce571

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• edit logging

  

  Michael J. Wilson

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  a33ee0f

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• fix logging

  

  Michael J. Wilson

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  1220e51

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• fix logging

  

  Michael J. Wilson

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  2203e7a

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• fix bugs

  

  Michael J. Wilson

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  ec3f505

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Commits on Aug 17, 2024

• fix bugs

  

  Michael J. Wilson

  committed
  4a0ca5b

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• fix

  

  Michael J. Wilson

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  203d803

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Commits on Aug 18, 2024

• logging fixes

  

  Michael J. Wilson

  committed
  ad1dc5c

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• fix

  

  Michael J. Wilson

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  a900b6f

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• add Baum-Welch log lines.

  

  Michael J. Wilson

  committed
  97138d1

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• fix

  

  Michael J. Wilson

  committed
  692b44d

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• fix logging.

  

  Michael J. Wilson

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  ff81c80

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• log bandwidth

  

  Michael J. Wilson

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  ee223f4

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• fix logging

  

  Michael J. Wilson

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  d91c1a9

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• fix

  

  Michael J. Wilson

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  002c887

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• fix logging

  

  Michael J. Wilson

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  253c332

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• fix logging bug

  

  Michael J. Wilson

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  78d539e

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• add TODO for gammas in phasing beta binomial

  

  Michael J. Wilson

  committed
  200816f

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• fix

  

  Michael J. Wilson

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  5127a64

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• fix

  

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  1c398c7

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• fix

  

  Michael J. Wilson

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  974b155

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• fix

  

  Michael J. Wilson

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  546b062

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• add hmrf logging

  

  Michael J. Wilson

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  2f2b85a

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• add cpas

  

  Michael J. Wilson

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  a68af44

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Commits on Aug 19, 2024

• log phasing baum welch.

  

  Michael J. Wilson

  committed
  87da6fe

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• fix

  

  Michael J. Wilson

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  79d9064

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• log initial alpha and tau

  

  Michael J. Wilson

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  78a6784

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• fix

  

  Michael J. Wilson

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  fda9a3b

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• fix

  

  Michael J. Wilson

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  1a3fb9a

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• fix

  

  Michael J. Wilson

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  3e65038

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• fix

  

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  a60cbcd

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• fix

  

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  340d978

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• fix

  

  Michael J. Wilson

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  98c77bc

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Commits on Aug 20, 2024

• write Weighted Beta Binom chain file

  

  Michael J. Wilson

  committed
  3d0b1f7

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• fix

  

  Michael J. Wilson

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  0e0ab66

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• finishing touches

  

  Michael J. Wilson

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  8bbc53e

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Commits on Aug 26, 2024

• ABC for emission models

  

  Michael J. Wilson

  committed
  68b6a85

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• abc for emission models

  

  Michael J. Wilson

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  34239f2

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• fix

  

  Michael J. Wilson

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  1328b64

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• fixes

  

  Michael J. Wilson

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  a837ed7

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• fix

  

  Michael J. Wilson

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  9aba148

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• fix chain logging

  

  Michael J. Wilson

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  f6137aa

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• fix

  

  Michael J. Wilson

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  852b504

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• gzip chains

  

  Michael J. Wilson

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  5b44d30

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• fix

  

  Michael J. Wilson

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  91bcc35

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• fix

  

  Michael J. Wilson

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  aa277ab

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• update instance counts.

  

  Michael J. Wilson

  committed
  9c0f301

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• fix

  

  Michael J. Wilson

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  0bece4f

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• fix

  

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  dd7376e

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• fix

  

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  4761002

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• fix

  

  Michael J. Wilson

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  1ee174d

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• cleanup before adding ARI for HMM states.

  

  Michael J. Wilson

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  86b0de3

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• precision on likelihood chain

  

  Michael J. Wilson

  committed
  a154b93

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• fix

  

  Michael J. Wilson

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  16d70fd

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• add HMM ARI

  

  Michael J. Wilson

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  827c67b

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• fix

  

  Michael J. Wilson

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  f987449

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  fd75633

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  3735c68

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• fix

  

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  f35cd5b

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• fix

  

  Michael J. Wilson

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  b6a2f59

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• make parent dirs for chains

  

  Michael J. Wilson

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  9db418b

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• fix

  

  Michael J. Wilson

  committed
  432e30f

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• add hamming distances

  

  Michael J. Wilson

  committed
  f3e55b9

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• fixes

  

  Michael J. Wilson

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  eeeca09

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• add # of states for hamming.

  

  Michael J. Wilson

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  a2804e6

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• fix

  

  Michael J. Wilson

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  5c8e767

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• fix increment bug.

  

  Michael J. Wilson

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  e99820d

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• fix

  

  Michael J. Wilson

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  2907248

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Commits on Aug 27, 2024

• fix

  

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  1f2d659

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• fix

  

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  6a66c88

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• fix

  

  Michael J. Wilson

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  d3f2c44

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• remove unused seed initialization from emission fitting.

  

  Michael J. Wilson

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  3f06b56

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• fix

  

  Michael J. Wilson

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  4824f93

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Commits on Aug 28, 2024

• fix

  

  Michael J. Wilson

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  097303a

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• fix

  

  Michael J. Wilson

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  6fdf302

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• log class imbalance and write chain for start_type=default.

  

  Michael J. Wilson

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  f6ada45

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• add weighted class balance

  

  Michael J. Wilson

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  b57880a

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• fix

  

  Michael J. Wilson

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Commits on Sep 3, 2024

• rm tar

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