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[ADAM-461] Fix ReferenceRegion and ReferencePosition impl #469

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merged 1 commit into from Nov 17, 2014

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@laserson
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laserson commented Nov 7, 2014

This commit mainly does 3 things:

  1. Fixes impl of ReferenceRegion.width.
  2. Removes Options from ReferencePosition.
  3. Corrected impl of liftOver. However, it now has different semantics: in all cases, the list of regions must be provided in genome order.
  4. Simplifies structure of case classes.

Fixes #461.

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@tdanford please review closely :)

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laserson commented Nov 7, 2014

@tdanford please review closely :)

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also, having a list of exons for a reverse-strand transcript still makes more sense to me to be in genome-order, and traversing it backwards (from 5' to 3'). What do you think?

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laserson commented Nov 7, 2014

also, having a list of exons for a reverse-strand transcript still makes more sense to me to be in genome-order, and traversing it backwards (from 5' to 3'). What do you think?

}
}
case class ReferencePositionWithOrientation(refPos: Option[ReferencePosition],
case class ReferencePositionWithOrientation(refPos: ReferencePosition,

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fnothaft Nov 7, 2014

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+1; this shouldn't have been an option.

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fnothaft Nov 7, 2014

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+1; this shouldn't have been an option.

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+1 (did I write this code originally? if so, it was me being even more of a Scala-n00b than I am now.)

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+1 (did I write this code originally? if so, it was me being even more of a Scala-n00b than I am now.)

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also, having a list of exons for a reverse-strand transcript still makes more sense to me to be in genome-order, and traversing it backwards (from 5' to 3'). What do you think?

Both ways seem reasonable to me. Why do you prefer them to be genome-ordered, instead of transcript-ordered?

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fnothaft commented Nov 7, 2014

also, having a list of exons for a reverse-strand transcript still makes more sense to me to be in genome-order, and traversing it backwards (from 5' to 3'). What do you think?

Both ways seem reasonable to me. Why do you prefer them to be genome-ordered, instead of transcript-ordered?

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ReferenceRegion enforces that start < end, so it seems like big/little endian-style confusion. To avoid that, my preference is that all objects are oriented in a way so that if you just glue them together, they are correct. Put another way, it's confusing to traverse the list of exons in order, but the sequence of the exon backwards.

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laserson commented Nov 7, 2014

ReferenceRegion enforces that start < end, so it seems like big/little endian-style confusion. To avoid that, my preference is that all objects are oriented in a way so that if you just glue them together, they are correct. Put another way, it's confusing to traverse the list of exons in order, but the sequence of the exon backwards.

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Put another way, it's confusing to traverse the list of exons in order, but the sequence of the exon backwards.

That's a good TL;DR. I would agree with your point.

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fnothaft commented Nov 7, 2014

Put another way, it's confusing to traverse the list of exons in order, but the sequence of the exon backwards.

That's a good TL;DR. I would agree with your point.

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@@ -30,7 +30,7 @@ class IndelTableSuite extends SparkFunSuite {
}
test("check for indels in a contig that doesn't exist") {
assert(indelTable.getIndelsInRegion(ReferenceRegion("0", 0L, 0L)).length === 0)
assert(indelTable.getIndelsInRegion(ReferenceRegion("0", 0L, 1L)).length === 0)

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Ok, test is back, and passes now.

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Ok, test is back, and passes now.

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Excellent. Thank you for catching the empty region!

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Excellent. Thank you for catching the empty region!

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* strand, else it will be on the positive strand.
* @return Returns an oriented reference region.
* @param referenceName The name of the sequence (chromosome) in the reference genome
* @param start The 0-based residue-coordinate for the start of the region

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@massie and I were talking about this in IRC, we really need to explain somewhere not in code what our coordinate conventions are. I mean, I like the comments, but we also need non-code versions of the same comments.

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@massie and I were talking about this in IRC, we really need to explain somewhere not in code what our coordinate conventions are. I mean, I like the comments, but we also need non-code versions of the same comments.

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Strongly agree with that.

Note, btw, that in my mental model, region.start should always be <
region.end.

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laserson Nov 12, 2014

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Strongly agree with that.

Note, btw, that in my mental model, region.start should always be <
region.end.

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Agreed -- the convention of "end < start" to designate negative-strand regions is messed up

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Agreed -- the convention of "end < start" to designate negative-strand regions is messed up

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I've started a rudimentary non-code writeup of the coordinate convention question here:
https://github.com/bigdatagenomics/adam/wiki/Coordinate-Conventions

Please feel free to (a) edit it, (b) tell me I'm wrong and get me to edit it some more, or (c) adapt it as content in some other location (the docs/ directory, Matt?)

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tdanford commented Nov 14, 2014

I've started a rudimentary non-code writeup of the coordinate convention question here:
https://github.com/bigdatagenomics/adam/wiki/Coordinate-Conventions

Please feel free to (a) edit it, (b) tell me I'm wrong and get me to edit it some more, or (c) adapt it as content in some other location (the docs/ directory, Matt?)

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Please feel free to (a) edit it, (b) tell me I'm wrong and get me to edit it some more, or (c) adapt it as content in some other location (the docs/ directory, Matt?)

I think the docs directory would be the best approach. We're trying to move documentation to there, so that it is autogenerated on each release.

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fnothaft commented Nov 14, 2014

Please feel free to (a) edit it, (b) tell me I'm wrong and get me to edit it some more, or (c) adapt it as content in some other location (the docs/ directory, Matt?)

I think the docs directory would be the best approach. We're trying to move documentation to there, so that it is autogenerated on each release.

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@laserson can you rebase? Then, I'll merge.

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fnothaft commented Nov 14, 2014

@laserson can you rebase? Then, I'll merge.

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Done.

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laserson commented Nov 14, 2014

Done.

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Build result: FAILURE

GitHub pull request #469 of commit 619ec42 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 207a1b3277d39d915e80d7e2f49fe5e5979a07f4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 207a1b3277d39d915e80d7e2f49fe5e5979a07f4 > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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GitHub pull request #469 of commit 619ec42 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 207a1b3277d39d915e80d7e2f49fe5e5979a07f4 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 207a1b3277d39d915e80d7e2f49fe5e5979a07f4 > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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Can you run the format-source script?

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fnothaft commented Nov 14, 2014

Can you run the format-source script?

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Done.

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laserson commented Nov 14, 2014

Done.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Nov 14, 2014

Jenkins, retest this please.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Nov 15, 2014

Jenkins, retest this please.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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GitHub pull request #469 of commit 9b8c7b0 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision ba61a5e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f ba61a5e > git rev-list cc683a5 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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@sknapp Can you take a look? This build has timed out several times. I'll test on my local machine to see if there's a problem with this changeset.

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fnothaft commented Nov 15, 2014

@sknapp Can you take a look? This build has timed out several times. I'll test on my local machine to see if there's a problem with this changeset.

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Builds fine on my local machine.

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laserson commented Nov 16, 2014

Builds fine on my local machine.

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If it's come to building locally :( any chance we can get this in as well?

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laserson commented Nov 17, 2014

If it's come to building locally :( any chance we can get this in as well?

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OK, I've upped the build timeout. Can you rebase this?

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fnothaft commented Nov 17, 2014

OK, I've upped the build timeout. Can you rebase this?

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Rebased.

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laserson commented Nov 17, 2014

Rebased.

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Build result: ABORTED

GitHub pull request #469 of commit 4ec66c7 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 28dc0d1063cc42a77951c19afe5841252369016e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 28dc0d1063cc42a77951c19afe5841252369016e > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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Build result: ABORTED

GitHub pull request #469 of commit 4ec66c7 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 28dc0d1063cc42a77951c19afe5841252369016e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 28dc0d1063cc42a77951c19afe5841252369016e > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result ABORTEDADAM-prb » 1.0.4,centos completed with result ABORTEDADAM-prb » 2.2.0,centos completed with result ABORTED
Test FAILed.

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Jenkins, retest this please.

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fnothaft commented Nov 17, 2014

Jenkins, retest this please.

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #469 of commit 4ec66c7 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 28dc0d1063cc42a77951c19afe5841252369016e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 28dc0d1063cc42a77951c19afe5841252369016e > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

AmplabJenkins commented Nov 17, 2014

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/413/

Build result: FAILURE

GitHub pull request #469 of commit 4ec66c7 automatically merged.[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-slave-01 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ > git rev-parse origin/pr/469/merge^{commit} # timeout=10Checking out Revision 28dc0d1063cc42a77951c19afe5841252369016e (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f 28dc0d1063cc42a77951c19afe5841252369016e > git rev-list f211b54 # timeout=10Triggering ADAM-prb » 2.3.0,centosTriggering ADAM-prb » 1.0.4,centosTriggering ADAM-prb » 2.2.0,centosADAM-prb » 2.3.0,centos completed with result FAILUREADAM-prb » 1.0.4,centos completed with result FAILUREADAM-prb » 2.2.0,centos completed with result FAILURE
Test FAILed.

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@laserson can you run scripts/format-source?

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fnothaft commented Nov 17, 2014

@laserson can you run scripts/format-source?

Uri Laserson
[ADAM-461] Fix ReferenceRegion and ReferencePosition impl
This commit mainly does 3 things:

1. Fixes impl of `ReferenceRegion.width`.

2. Removes `Option`s from `ReferencePosition`.

3. Corrected impl of liftOver.  However, it now has different semantics: in all cases, the list of regions must be provided in genome order.

4. Simplifies structure of case classes.

Fixes #461.
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argh! sorry...fixed it

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laserson commented Nov 17, 2014

argh! sorry...fixed it

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Test PASSed.
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Test PASSed.

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Test PASSed.
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Test PASSed.

fnothaft added a commit that referenced this pull request Nov 17, 2014

Merge pull request #469 from laserson/ADAM-461
[ADAM-461] Fix ReferenceRegion and ReferencePosition impl

@fnothaft fnothaft merged commit 51610d1 into bigdatagenomics:master Nov 17, 2014

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Merged! Thanks @laserson, and thanks for the patience with the build timeouts...

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fnothaft commented Nov 17, 2014

Merged! Thanks @laserson, and thanks for the patience with the build timeouts...

@laserson laserson deleted the laserson:ADAM-461 branch Dec 2, 2014

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