/htsjdk

Removed gelitext package (deprecated) #753

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merged 1 commit into from Jan 10, 2017

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@magicDGS @coveralls @lbergelson @droazen @vdauwera
@magicDGS
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magicDGS commented Nov 24, 2016 • edited

Description

Cleaning up some long-deprecated classes from gelitext, tests and usages. Found in #707.

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)
@coveralls

coveralls commented Nov 24, 2016

Coverage Status

Coverage increased (+0.03%) to 70.036% when pulling d8c26d5 on magicDGS:dgs_remove_gelitext into de27f18 on samtools:master.
@lbergelson
Contributor

lbergelson commented Nov 30, 2016

Is there anyone in the world who still uses Geli? If so... please comment on this pull request...
@magicDGS magicDGS removed gelitext package and usages

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continuous-integration/travis-ci/pr — The Travis CI build passed
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coverage/coveralls — Coverage increased (+0.02%) to 70.031%
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76d81d1
@magicDGS
Contributor

magicDGS commented Dec 1, 2016

Updated branch to remove conflicts.
@coveralls

coveralls commented Dec 1, 2016

Coverage Status

Coverage increased (+0.02%) to 70.031% when pulling 76d81d1 on magicDGS:dgs_remove_gelitext into 6469969 on samtools:master.
@droazen
Contributor

droazen commented Dec 13, 2016 • edited

@vdauwera or @jrobinso Do either of you have an opinion on this one? GATK3 still has support for this format, but I'm not sure there are any users left.

vdauwera was assigned by droazen Dec 13, 2016

@vdauwera
Contributor

vdauwera commented Dec 13, 2016

No one has ever asked about it that I can remember, so I'd be comfortable killing it.
@droazen
Contributor

droazen commented Dec 13, 2016

@vdauwera Full disclosure: there is an actual tool in GATK3 that would have to be deleted if this goes in (VcfToGeliText)
@vdauwera
Contributor

vdauwera commented Dec 13, 2016

Is that a private tool? I've never even come across it that I can recall...
@droazen
Contributor

droazen commented Dec 13, 2016

Yes, it's a private tool
@vdauwera
Contributor

vdauwera commented Dec 13, 2016

Then kill away...
@magicDGS
Contributor

magicDGS commented Jan 9, 2017

Everybody agrees on this?
@vdauwera
Contributor

vdauwera commented Jan 9, 2017

👍

@droazen droazen merged commit 9c5cbf6 into samtools:master Jan 10, 2017
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continuous-integration/travis-ci/pr The Travis CI build passed
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coverage/coveralls Coverage increased (+0.02%) to 70.031%
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