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Commits on Jul 3, 2024

• adding details on readthedocs to dev documentation

  Jeltje

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• debugging readthedocs

  Jeltje

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• debugging readthedocs

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• debugging readthedocs

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• debugging readthedocs

  Jeltje

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• adding yaml for readhtedocs

  Jeltje

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• correcting rst format

  Jeltje

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Commits on Jun 28, 2024

• Update modules.rst LRGASP highlight

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  anbrooks

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Commits on Feb 15, 2024

• fix BrooksLabUCSC#180, thanks Colette

  Jeltje

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Commits on Jan 18, 2024

• fixed BrooksLabUCSC#318; updated faq

  Jeltje

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Commits on Dec 11, 2023

• added comment text to clarify strand and splice orientation

  Jeltje

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Commits on Dec 7, 2023

• CONTRIBUTING.md

  Jeltje

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Commits on Dec 5, 2023

• Create CONTRIBUTING

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• Create CODE_OF_CONDUCT.md

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Commits on Sep 29, 2023

• Merge pull request BrooksLabUCSC#251 from listen2099/patch-1

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  Jeltje

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• Merge branch 'master' into patch-1

  Jeltje

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• Merge pull request BrooksLabUCSC#300 from BrooksLabUCSC/refactor

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  Jeltje

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• updated arg calls to full words; simplified parser. This code still needs to be refactored, it has functions and main code interspersed

  Jeltje

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Commits on Sep 15, 2023

• added underscore in isoform name when no annotation is present for chromosome; fixes BrooksLabUCSC#280

  Jeltje

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Commits on Sep 13, 2023

• improved import statement in correct

  Jeltje

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• Merge pull request BrooksLabUCSC#297 from BrooksLabUCSC/refactor

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  Jeltje

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• adding yeast specific parameter example to flair collapse

  Jeltje

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• changed output directory name in makefile

  Jeltje

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• Merge pull request BrooksLabUCSC#296 from BrooksLabUCSC/master

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  Jeltje

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• Merge pull request BrooksLabUCSC#295 from diekhans/test_fixes_etc

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  Jeltje

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• added pands to requirments

  diekhans

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• give useful message instead of just run first test if no test is specified

  diekhans

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• remove executable bits from makefile

  diekhans

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• added explict parameters to an inner function to work around a bug in pythong 3.11 that cause bed_to_sequence to never complete in the test case

  diekhans

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• added gitignore and emacs conf to use FLAIR tab mode

  diekhans

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Commits on Sep 12, 2023

• added missing pipettor dependency

  diekhans

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Commits on Sep 8, 2023

• Merge pull request BrooksLabUCSC#292 from BrooksLabUCSC/refactor

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  Jeltje

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• fixes BrooksLabUCSC#291. gtfToSSBed now dies with appropriate error message if the input file does not look like gtf

  Jeltje

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• added TODO comment

  Jeltje

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• fixes BrooksLabUCSC#290. Now creates a single-nonsense-entry NCLS intervaltree if no junctions are found, which stops the program from erroring out later. Still to do: Rename the remaining c1, c2 a…

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