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Commits on Mar 3, 2023

• minor changes

  Jeltje

  committed
  5c1f668

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Commits on Mar 2, 2023

• merging Alison documentation updates

  Jeltje

  committed
  c300ee1

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Commits on Dec 8, 2022

• adding conversion scripts to bin. These are suggested by count_sam_transcripts when it fails

  Jeltje

  committed
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Commits on Oct 20, 2022

• removed redundant color assignment from plot_isoform_usage

  Jeltje

  committed
  595b8a3

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Commits on Oct 18, 2022

• removed deFLAIR from manual, added details on check_splice with annotation_reliant in diffExp

  Jeltje

  committed
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Commits on Oct 1, 2022

• documentation and usage statement corrections for helper code

  Jeltje

  committed
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Commits on Sep 30, 2022

• removed file path inputs to flair module parameters to simplify code and input. With conda or docker install these are never necessary

  Jeltje

  committed
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• removed psl from main Flair to simplify code and inputs. Conversion tools remain in bin directory. Programs in src directory still take psl but renamed tools to avoid confusion

  Jeltje

  committed
  7b3b509

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• added cannot_verify output file to ssCorrect to avoid flair correct silently removing reads for which the chromosome cannot be found in the input annotation

  Jeltje

  committed
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Commits on Sep 13, 2022

• flake8 whitespace and unused variables

  Jeltje

  committed
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Commits on Aug 8, 2022

• more commandline programs for pip

  Jeltje

  committed
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Commits on Jul 15, 2022

• removing python extensions from manual

  Jeltje

  committed
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• moving independent scripts to bin, linking scripts listed in manual to bin

  Jeltje

  committed
  dc02eb1

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• renaming bin scripts

  Jeltje

  committed
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• changes for pip install

  Jeltje

  committed
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Commits on Jul 14, 2022

• removed bin CRLF line terminators

  Jeltje

  committed
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• remove obsolete code from bin

  Jeltje

  committed
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• moving all helper programs to src

  Jeltje

  committed
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Commits on Jul 6, 2022

• replaced script.py with actual script name

  Jeltje

  committed
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Commits on Jun 30, 2022

• In collapse run alignment as pipe instead of saving to file (see e.g. issue 160); replace unchecked subprocess.calls with check_calls

  Jeltje

  committed
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• Merge pull request BrooksLabUCSC#203 from xyloforce/master

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  Jeltje

  authored
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Commits on Jun 27, 2022

• readding isoforms_by_proportion

  Jeltje

  committed
  9c08641

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Commits on Jun 3, 2022

• fixed args for collapse

  xyloforce

  committed
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Commits on Feb 8, 2022

• samjuncs update

  belgravia

  committed
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Commits on Feb 3, 2022

• longshot specific variant integration

  belgravia

  committed
  3d71f56

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Commits on Nov 22, 2021

• cigar H bug fixed

  belgravia

  committed
  123b661

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Commits on Oct 25, 2021

• annotation_reliant lrgasp

  belgravia

  committed
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Commits on Jul 19, 2021

• quick bug fix

  belgravia

  committed
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Commits on Jun 30, 2020

• bugs with threeprime fixd

  belgravia

  committed
  0f71b5f

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Commits on Jun 29, 2020

• small fixes, added in a 3prime option for collapse

  belgravia

  committed
  2f8df51

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Commits on May 29, 2020

• other ways to run flair added

  belgravia

  committed
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Commits on Apr 23, 2020

• shebang headers added

  belgravia

  committed
  730cce4

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Commits on Apr 7, 2020

• stringent collapse option is working again

  belgravia

  committed
  5eb7c11

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Commits on Mar 18, 2020

• fixed typos in count_sam_transcripts.py

  belgravia

  committed
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Commits on Mar 13, 2020

• bug fixes in downstream scripts

  belgravia

  committed
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