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Bugfixes and code optimization #150

Merged
merged 8 commits into from
Jan 31, 2022
Merged

Bugfixes and code optimization #150

merged 8 commits into from
Jan 31, 2022

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kmnip
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@kmnip kmnip commented Jan 26, 2022

  • add missing package names (fixes requirements.txt is incomplete #135)
  • create BAM instead of SAM in transcriptome mode (undo changes in 3d046e3)
  • set default file compression level to 1 (previously level 6)
  • optimize code for head/tail length calculation in transcriptome mode
  • optimize code for quantification

@kmnip kmnip requested a review from SaberHQ January 26, 2022 22:28
@kmnip kmnip self-assigned this Jan 26, 2022
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SaberHQ approved these changes Jan 31, 2022
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Thanks for the pull request @kmnip . I tested all suggested edits and everything works good. I will merge the pull request.

@SaberHQ SaberHQ merged commit ff052d5 into bcgsc:master Jan 31, 2022
@SaberHQ SaberHQ mentioned this pull request Mar 28, 2022
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requirements.txt is incomplete
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