fix deprecation warnings #985

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ryan-williams opened this Issue Mar 28, 2016 · 5 comments

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ryan-williams commented Mar 28, 2016

I see many deprecated avro-record field-accesses laying around, we should fix them.

@ryan-williams ryan-williams self-assigned this Mar 28, 2016

ryan-williams added a commit to ryan-williams/adam that referenced this issue Mar 28, 2016

fnothaft added a commit that referenced this issue Mar 29, 2016

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heuermh Apr 7, 2016

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@ryan-williams was this fixed by #986 or do you have more fixing in mind? :)

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heuermh commented Apr 7, 2016

@ryan-williams was this fixed by #986 or do you have more fixing in mind? :)

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ryan-williams Apr 20, 2016

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Running mvn package from HEAD atm, I see two remaining warnings:

[WARNING] /Users/ryan/c/adam/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala:38: warning: object DecadentRead in package rich is deprecated: Use RichAlignmentRecord wherever possible in new development.
[WARNING]     val bqsr = new BaseQualityRecalibration(cloy(reads), snps)
[WARNING]                                             ^
[WARNING] /Users/ryan/c/adam/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala:58: warning: object DecadentRead in package rich is deprecated: Use RichAlignmentRecord wherever possible in new development.
[WARNING]     val bqsr = new BaseQualityRecalibration(cloy(reads), snps)
[WARNING]                                             ^
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ryan-williams commented Apr 20, 2016

Running mvn package from HEAD atm, I see two remaining warnings:

[WARNING] /Users/ryan/c/adam/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala:38: warning: object DecadentRead in package rich is deprecated: Use RichAlignmentRecord wherever possible in new development.
[WARNING]     val bqsr = new BaseQualityRecalibration(cloy(reads), snps)
[WARNING]                                             ^
[WARNING] /Users/ryan/c/adam/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala:58: warning: object DecadentRead in package rich is deprecated: Use RichAlignmentRecord wherever possible in new development.
[WARNING]     val bqsr = new BaseQualityRecalibration(cloy(reads), snps)
[WARNING]                                             ^
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fnothaft Apr 20, 2016

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Running mvn package from HEAD atm, I see two remaining warnings:

Those will be hanging around until we refactor out the DecadentRead class.
I added the deprecation flags to DecadentRead so that no one introduces more code using it, but refactoring it out looks like a fair bit of work, so I've been punting on it for a while.

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fnothaft commented Apr 20, 2016

Running mvn package from HEAD atm, I see two remaining warnings:

Those will be hanging around until we refactor out the DecadentRead class.
I added the deprecation flags to DecadentRead so that no one introduces more code using it, but refactoring it out looks like a fair bit of work, so I've been punting on it for a while.

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Cool, seems like #577 is the issue for that, will close this, thx

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ryan-williams commented Apr 20, 2016

Cool, seems like #577 is the issue for that, will close this, thx

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fnothaft Apr 20, 2016

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SGTM!

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fnothaft commented Apr 20, 2016

SGTM!

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