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Convert FastqToSam and RevertSam to use PicardHtsPath #1794

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merged 18 commits into from
Apr 21, 2022

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markjschreiber
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Description

Enables FastqToSam and RevertSam applications to use paths for input files.


Checklist (never delete this)

Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.

Content

  • Added or modified tests to cover changes and any new functionality
  • Edited the README / documentation (if applicable)
  • All tests passing on Travis

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  • Final thumbs-up from reviewer
  • Rebase, squash and reword as applicable

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src/main/java/picard/sam/FastqToSam.java Show resolved Hide resolved
src/main/java/picard/sam/FastqToSam.java Outdated Show resolved Hide resolved
src/main/java/picard/sam/RevertSam.java Outdated Show resolved Hide resolved
src/test/java/picard/sam/AbstractAlignmentMergerTest.java Outdated Show resolved Hide resolved
@markjschreiber
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Hi there, just wondering if this could be merged. I have some more conversions that I'll start working on soon.

@gbggrant
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Looks good to me - @yfarjoun do you want to re-review?

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@yfarjoun yfarjoun left a comment

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👍

@gbggrant gbggrant merged commit d784ca3 into broadinstitute:master Apr 21, 2022
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3 participants