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added start and end values to Interval Trait. Used for IntervalRDD #931

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merged 1 commit into from Feb 9, 2016

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akmorrow13 commented Feb 4, 2016

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AmplabJenkins Feb 4, 2016

Can one of the admins verify this patch?

AmplabJenkins commented Feb 4, 2016

Can one of the admins verify this patch?

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Jenkins, add to whitelist.

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fnothaft commented Feb 4, 2016

Jenkins, add to whitelist.

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Jenkins, test this please.

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fnothaft commented Feb 4, 2016

Jenkins, test this please.

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Also, +1 from me.

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fnothaft commented Feb 4, 2016

Also, +1 from me.

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Do we still need width if we have start and end? Do we need or want to support open ended intervals? Intervals around the origin in circular genomes? Zero-based or one-based coordinate systems? etc.

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heuermh commented Feb 4, 2016

Do we still need width if we have start and end? Do we need or want to support open ended intervals? Intervals around the origin in circular genomes? Zero-based or one-based coordinate systems? etc.

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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/1073/
Test PASSed.

AmplabJenkins commented Feb 4, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1073/
Test PASSed.

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Do we still need width if we have start and end?

Would probably make sense to define width = end - start

Do we need or want to support open ended intervals? Zero-based or one-based coordinate systems? etc.

We decided early on that we were going to be consistently 0-based, open ended inside of ADAM.

Intervals around the origin in circular genomes?

I wouldn't worry about this for now since no one's asked for it and it adds a fair bit of complexity, but it is something to consider later.

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fnothaft commented Feb 4, 2016

@heuermh

Do we still need width if we have start and end?

Would probably make sense to define width = end - start

Do we need or want to support open ended intervals? Zero-based or one-based coordinate systems? etc.

We decided early on that we were going to be consistently 0-based, open ended inside of ADAM.

Intervals around the origin in circular genomes?

I wouldn't worry about this for now since no one's asked for it and it adds a fair bit of complexity, but it is something to consider later.

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AmplabJenkins Feb 9, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1076/
Test PASSed.

AmplabJenkins commented Feb 9, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1076/
Test PASSed.

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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/1077/
Test PASSed.

AmplabJenkins commented Feb 9, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1077/
Test PASSed.

@erictu erictu referenced this pull request Feb 9, 2016

Merged

Major Feature Upgrades #74

@fnothaft fnothaft merged commit 92ea747 into bigdatagenomics:master Feb 9, 2016

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