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Adding fragment InFormatter for Bowtie tab5 format #1522

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merged 1 commit into from May 31, 2017

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@heuermh
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heuermh commented May 12, 2017

I was mistaken earlier that supporting tab6 would be sufficient for bowtie and bowtie2 support in cannoli. Tab5 format is req'd for the bowtie --12 argument.

See bigdatagenomics/cannoli#33

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coveralls May 12, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.879% when pulling e3084d8 on heuermh:tab5-formatter into 18191f9 on bigdatagenomics:master.

coveralls commented May 12, 2017

Coverage Status

Coverage decreased (-0.1%) to 81.879% when pulling e3084d8 on heuermh:tab5-formatter into 18191f9 on bigdatagenomics:master.

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AmplabJenkins May 12, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1993/
Test PASSed.

AmplabJenkins commented May 12, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
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Test PASSed.

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LGTM! Have you tested this downstream?

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fnothaft commented May 12, 2017

LGTM! Have you tested this downstream?

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heuermh May 15, 2017

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Have you tested this downstream?

Not working yet, will update this issue with link to cannoli pull request when ready

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heuermh commented May 15, 2017

Have you tested this downstream?

Not working yet, will update this issue with link to cannoli pull request when ready

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fnothaft May 24, 2017

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Ping @heuermh about testing. Let me know if this is tested and good to merge.

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fnothaft commented May 24, 2017

Ping @heuermh about testing. Let me know if this is tested and good to merge.

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heuermh May 24, 2017

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The code here tests fine and looks ok, but there appears to be a problem streaming to Bowtie
bigdatagenomics/cannoli#42 (comment)

Reported as
BenLangmead/bowtie#51

Wouldn't hurt to merge this now and track the issue with Bowtie in the cannoli repo.

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heuermh commented May 24, 2017

The code here tests fine and looks ok, but there appears to be a problem streaming to Bowtie
bigdatagenomics/cannoli#42 (comment)

Reported as
BenLangmead/bowtie#51

Wouldn't hurt to merge this now and track the issue with Bowtie in the cannoli repo.

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coveralls May 30, 2017

Coverage Status

Coverage increased (+0.2%) to 82.2% when pulling ff99571 on heuermh:tab5-formatter into b0c5c5f on bigdatagenomics:master.

coveralls commented May 30, 2017

Coverage Status

Coverage increased (+0.2%) to 82.2% when pulling ff99571 on heuermh:tab5-formatter into b0c5c5f on bigdatagenomics:master.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2073/
Test PASSed.

AmplabJenkins commented May 30, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2073/
Test PASSed.

@fnothaft fnothaft merged commit bbd695e into bigdatagenomics:master May 31, 2017

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codacy/pr Good work! A positive pull request.
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coverage/coveralls Coverage increased (+0.2%) to 82.2%
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default Merged build finished.
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Merged! Thanks @heuermh!

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fnothaft commented May 31, 2017

Merged! Thanks @heuermh!

@heuermh heuermh deleted the heuermh:tab5-formatter branch May 31, 2017

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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