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Clean up ReferenceRegion.scala and add thresholded overlap and covers #1484

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devin-petersohn commented Apr 10, 2017

Partially resolves #1473 and fully resolves #1474.

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Coverage increased (+0.1%) to 81.779% when pulling 6855c05 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 10, 2017

Coverage Status

Coverage increased (+0.1%) to 81.779% when pulling 6855c05 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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Once this is merged in, I will update #1324 to reflect the ability to use thresholds to join.

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devin-petersohn commented Apr 10, 2017

Once this is merged in, I will update #1324 to reflect the ability to use thresholds to join.

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Coverage increased (+0.2%) to 81.8% when pulling af70a8d on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 10, 2017

Coverage Status

Coverage increased (+0.2%) to 81.8% when pulling af70a8d on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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@devin-petersohn devin-petersohn changed the title from Issue#1473 threshold overlaps to Clean up ReferenceRegion.scala and add thresholded overlap and covers Apr 10, 2017

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fnothaft Apr 15, 2017

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Hi @devin-petersohn! Is this ready for another round of review?

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fnothaft commented Apr 15, 2017

Hi @devin-petersohn! Is this ready for another round of review?

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devin-petersohn Apr 16, 2017

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I have actually encountered another couple of distance based operations that belong here. Everything is ready, but I want to make sure there aren't any more that I need before I ask for another review round. I will let you know as soon as this is done.

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devin-petersohn commented Apr 16, 2017

I have actually encountered another couple of distance based operations that belong here. Everything is ready, but I want to make sure there aren't any more that I need before I ask for another review round. I will let you know as soon as this is done.

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Coverage Status

Coverage decreased (-0.03%) to 81.603% when pulling cdcb926 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 17, 2017

Coverage Status

Coverage decreased (-0.03%) to 81.603% when pulling cdcb926 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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@devin-petersohn devin-petersohn requested review from heuermh and fnothaft Apr 18, 2017

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Coverage increased (+0.3%) to 81.928% when pulling 5a0e19e on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

coveralls commented Apr 24, 2017

Coverage Status

Coverage increased (+0.3%) to 81.928% when pulling 5a0e19e on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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Coverage increased (+0.3%) to 81.959% when pulling 8a2e011 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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Coverage increased (+0.3%) to 81.959% when pulling 8a2e011 on devin-petersohn:issue#1473ThresholdOverlaps into 93b32c6 on bigdatagenomics:master.

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@heuermh

LGTM, suggested a few minor doc fixes

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala Outdated
Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala Outdated
assert(referenceName == region.referenceName, "Cannot compute convex hull of regions on different references.")
ReferenceRegion(referenceName, min(start, region.start), max(end, region.end))
def hull(other: ReferenceRegion): ReferenceRegion = {
require(sameStrand(other), "Cannot compute convex hull of differently oriented regions.")

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heuermh Apr 24, 2017

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For require messages, use phrases or sentences or exclamations, but not all three :)

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heuermh Apr 24, 2017

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For require messages, use phrases or sentences or exclamations, but not all three :)

Show outdated Hide outdated adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala Outdated
Cleaning up code in ReferenceRegion.scala, adding threshold options
More cleanup and adding isNearby

Adding threshold logic to overlaps and covers

Replacing var with fold call

Adding overlapsBy and coversBy and related tests

Adding subtract, addressing reviewer comments

Addressing reviewer comments

Addressing reviewer comments
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devin-petersohn Apr 24, 2017

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Squashed and rebased. Thanks for the feedback @fnothaft and @heuermh!

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devin-petersohn commented Apr 24, 2017

Squashed and rebased. Thanks for the feedback @fnothaft and @heuermh!

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fnothaft Apr 24, 2017

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Thanks @devin-petersohn! I will merge this once tests pass.

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fnothaft commented Apr 24, 2017

Thanks @devin-petersohn! I will merge this once tests pass.

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Coverage Status

Coverage decreased (-0.06%) to 81.726% when pulling ebfc510 on devin-petersohn:issue#1473ThresholdOverlaps into 1fb57a3 on bigdatagenomics:master.

coveralls commented Apr 24, 2017

Coverage Status

Coverage decreased (-0.06%) to 81.726% when pulling ebfc510 on devin-petersohn:issue#1473ThresholdOverlaps into 1fb57a3 on bigdatagenomics:master.

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@fnothaft fnothaft merged commit 5b6a109 into bigdatagenomics:master Apr 24, 2017

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coverage/coveralls Coverage decreased (-0.06%) to 81.726%
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codacy/pr Good work! A positive pull request.
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fnothaft Apr 24, 2017

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Merged! Thanks @devin-petersohn!

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fnothaft commented Apr 24, 2017

Merged! Thanks @devin-petersohn!

@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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