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Expose shadowed logic#11

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CiaranOMara wants to merge 23 commits intoowenjm:masterowenjm/damidseq_pipeline:masterfrom CiaranOMara:developCiaranOMara/damidseq_pipeline:developCopy head branch name to clipboard

+436-327

Commits

Commits on Oct 21, 2020

• Add .gitignore

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  committed
  e7f2ba7

Commits on Oct 22, 2020

• New line at end of file

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• Tab spaces

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• Copyright character

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• Typos

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• Use warnings

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  15117ef

• Remove unused variables

  CiaranOMara

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  91ca75c

• Move reset defaults into sub routine

  CiaranOMara

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  816e37a

• Expose shadowed logic of save defaults

  CiaranOMara

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  5f3dc47

• Expose shadowed logic of extend reads

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  3102f72

• Expose shadowed logic of extend reads full

  CiaranOMara

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  486346a

• Remove double check for bowtie

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  b4342a6

Commits on Apr 11, 2021

• Expose shadowed logic of align sequences

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  dad28be

• Convert statement to compound for consistency

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  78e4808

• Return score early

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• Print empty string

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• Remove unnecessary else block

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• Comments for executable_check

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  cf3f139

• Comments for find_norm_factor

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• Comments for find_quants

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  3e6835a

• Extract config directory setup

  CiaranOMara

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  fa702b1

• Extract listing of defaults

  CiaranOMara

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Commits on Oct 22, 2022

• Filter out header comments from SAM/BAM files

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  3946b09