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Keep cigartuples#108

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heidi-holappa wants to merge 46 commits intomasterablab/IsoQuant:masterfrom keep_cigartuplesablab/IsoQuant:keep_cigartuplesCopy head branch name to clipboard

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Commits on Aug 8, 2023

• keep cigartuples in read assignment

  andrewprzh

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  1b26e04

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Commits on Aug 17, 2023

• template for transcript correction

  andrewprzh

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  27f52fe

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Commits on Aug 21, 2023

• Add initial implementation for transcript_splice_site_corrector and unittests

  heidi-holappa

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Commits on Aug 22, 2023

• Fix issues with two unittests

  heidi-holappa

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  bd52a52

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• Fix issue with two datastructures having the same var name

  heidi-holappa

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  99c9d39

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• Refactor code into separate functions

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• Refactor code into separate functions

  heidi-holappa

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  321be9c

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• Expand tests for untested functions

  heidi-holappa

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  f30996b

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• Expand unittests

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  3f8aa16

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• expand unittests

  heidi-holappa

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  3061f0f

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• Fix key-issue in splice_site_dict

  heidi-holappa

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• Add threshold verification to conservative strategy

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• Add constant for threshold to args

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  af81624

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• Update function name

  heidi-holappa

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  2740474

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• fix cigartuples, can be None sometimes

  andrewprzh

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Commits on Aug 23, 2023

• Add logger.debug to see corrected exons

  heidi-holappa

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  07ab569

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• Merge branch 'keep_cigartuples' of github.com:ablab/IsoQuant into keep_cigartuples

  heidi-holappa

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  c8efee0

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• Add logger.debug to see corrected exons

  heidi-holappa

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  7953ff3

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• Add logger.debug to see corrected exons

  heidi-holappa

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  bec61f8

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• Add logger.debug to see corrected exons

  heidi-holappa

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  8e46fc1

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• Add logger.debug to see indel calc

  heidi-holappa

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  0359146

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• Add debugging to see matching cases list

  heidi-holappa

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  bc91708

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• Add debugger to cases with no cigartuples

  heidi-holappa

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Commits on Aug 24, 2023

• add debug line to verify if cigartuples are found on some reads

  heidi-holappa

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Commits on Aug 25, 2023

• Move debug to correct transcripts

  heidi-holappa

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  6e217ec

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• Move debug to correct transcripts

  heidi-holappa

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  82fdc3a

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• Move debug to correct transcripts

  heidi-holappa

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  20440ae

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• Move debug to correct transcripts

  heidi-holappa

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  83f5ae6

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• Move debug to correct transcripts

  heidi-holappa

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  f8f363f

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• Fix bug with dict key ref

  heidi-holappa

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  b37f59b

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• Add test for GraphBasedModelConstructor

  heidi-holappa

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  8c240f4

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• Check for abs value

  heidi-holappa

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  2360b62

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• Expand unittests for GraphBaseModelConstructor method

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  898f75c

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• Improve debugger stdouts

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Commits on Aug 28, 2023

• Update unittest after changing constant positioning

  heidi-holappa

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• Move WINDOW_SIZE to main func

  heidi-holappa

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• Move const WINDOW_SIZE upper

  heidi-holappa

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  9e2c29d

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• Change division to multiplication

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  5c22578

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• Expand tests

  heidi-holappa

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  46d01bb

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Commits on Aug 29, 2023

• Shorten key name

  heidi-holappa

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  5a90864

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• Update tests after key name change

  heidi-holappa

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  47ca8b3

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• fix cigartuples exactly where they needed to be

  andrewprzh

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  b825a5c

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Commits on Aug 30, 2023

• Change idx correction for FASTA extract

  heidi-holappa

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  3c07e17

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• Fix unittests after fixing issue with chr_record idx-correction

  heidi-holappa

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  ce52d63

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• Merge branch 'keep_cigartuples' of github.com:ablab/IsoQuant into keep_cigartuples

  heidi-holappa

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• Remove unneeded logger.debugs

  heidi-holappa

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