Clean up `org.bdgenomics.adam.rich` package. #1263

Merged
merged 3 commits into from Nov 16, 2016

Conversation

Projects
None yet
3 participants
@fnothaft
Member

fnothaft commented Nov 12, 2016

Towards #1083.

  • Added scaladoc to all classes/methods that were missing docs.
  • Deprecated ReferenceSequenceContext
  • Deprecated implicit conversions to/from RichAlignmentRecord and eliminated dead code.
  • Made RichCigar package private to org.bdgenomics.adam. It is only used in org.bdgenomics.algorithms.consensus. I considered moving it over, but decided to keep all "enriched" classes in org.bdgenomics.adam.rich. I did eliminate the RichCigar singleton and make RichCigar a case class, while moving the only non-apply method over to org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator as a private method.

b4f0eeb deletes org.bdgenomics.adam.rich.RichGenotype, which is unused. I wasn't sure if we wanted to do this, as RichGenotype is kinda useful. Thoughts?

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 12, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1593/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 55addc94198bce4b105c33c15976d7529cb63dc3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision 55addc94198bce4b105c33c15976d7529cb63dc3 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 55addc94198bce4b105c33c15976d7529cb63dc3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1593/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 55addc94198bce4b105c33c15976d7529cb63dc3 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision 55addc94198bce4b105c33c15976d7529cb63dc3 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 55addc94198bce4b105c33c15976d7529cb63dc3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft referenced this pull request Nov 12, 2016

Closed

Clean up packages #1083

6 of 6 tasks complete
@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 13, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1594/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d724aca562c48dd2edb6f8ee38adb65ce39c02b8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision d724aca562c48dd2edb6f8ee38adb65ce39c02b8 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d724aca562c48dd2edb6f8ee38adb65ce39c02b8First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1594/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains d724aca562c48dd2edb6f8ee38adb65ce39c02b8 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision d724aca562c48dd2edb6f8ee38adb65ce39c02b8 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d724aca562c48dd2edb6f8ee38adb65ce39c02b8First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 14, 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/1596/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1596/
Test PASSed.

@@ -80,7 +80,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {
assert(adamVC.genotypes.size === 0)
- val variant = adamVC.variant
+ val variant = adamVC.variant.variant

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

Do I have it right in that these nested accesses weren't necessary before because of the implicit conversion?

@heuermh

heuermh Nov 14, 2016

Member

Do I have it right in that these nested accesses weren't necessary before because of the implicit conversion?

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

Correct.

@fnothaft

fnothaft Nov 14, 2016

Member

Correct.

*/
-
-case class ReferenceSequenceContext(pos: Option[ReferencePosition], referenceBase: Option[Char], cigarElement: CigarElement, cigarElementOffset: Int)
+@deprecated("don't use ReferenceSequenceContext in new development",

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

What is the time limit on this deprecation? Is there a reason not to remove it now?

@heuermh

heuermh Nov 14, 2016

Member

What is the time limit on this deprecation? Is there a reason not to remove it now?

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

We've got a ticket #577 for this. The long and short of it is that there's a lot of nasty code that came in from DecadentRead when BQSR was added, and it is a fairly involved refactor.

@fnothaft

fnothaft Nov 14, 2016

Member

We've got a ticket #577 for this. The long and short of it is that there's a lot of nasty code that came in from DecadentRead when BQSR was added, and it is a fairly involved refactor.

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

Thanks, I'm good since there is an issue to track

@heuermh

heuermh Nov 14, 2016

Member

Thanks, I'm good since there is an issue to track

@@ -92,7 +92,7 @@ object VariantContext {
* @return VariantContext corresponding to the data above.
*/
def apply(kv: (ReferencePosition, Variant, Iterable[Genotype], Option[DatabaseVariantAnnotation])): VariantContext = {
- new VariantContext(kv._1, kv._2, kv._3, kv._4)
+ new VariantContext(kv._1, RichVariant(kv._2), kv._3, kv._4)

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

Do we need to always wrap in RichVariant or should it be left to a later map after load if the caller needs it?

@heuermh

heuermh Nov 14, 2016

Member

Do we need to always wrap in RichVariant or should it be left to a later map after load if the caller needs it?

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

I think we could drop the rich variant, but I'm not entirely sure.

@fnothaft

fnothaft Nov 14, 2016

Member

I think we could drop the rich variant, but I'm not entirely sure.

+ @deprecated("Use explicit coversion wherever possible in new development.",
+ since = "0.21.0")

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

As above, what is the time limit on these deprecations? Is there a reason not to remove them now?

@heuermh

heuermh Nov 14, 2016

Member

As above, what is the time limit on these deprecations? Is there a reason not to remove them now?

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

See above/#577.

@fnothaft

fnothaft Nov 14, 2016

Member

See above/#577.

-
- def ploidy: Int = genotype.getAlleles.size
-
- def getType: GenotypeType = {

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

There is so much difficulty explaining what the different types mean I don't find GenotypeType very useful.

Hail defines even more genotype flags

genotype field definition
isHomRef true if this call is 0/0
isHet true if this call is heterozygous
isHetRef true if this call is 0/k with k>0
isHetNonRef true if this call is j/k with j>0
isHomVar true if this call is j/j with j>0
isCalledNonRef true if either isHet or isHomVar is true
isCalled true if the genotype is not ./.
isNotCalled true if the genotype is ./.

and still doesn't distinguish partial no-calls.

@heuermh

heuermh Nov 14, 2016

Member

There is so much difficulty explaining what the different types mean I don't find GenotypeType very useful.

Hail defines even more genotype flags

genotype field definition
isHomRef true if this call is 0/0
isHet true if this call is heterozygous
isHetRef true if this call is 0/k with k>0
isHetNonRef true if this call is j/k with j>0
isHomVar true if this call is j/j with j>0
isCalledNonRef true if either isHet or isHomVar is true
isCalled true if the genotype is not ./.
isNotCalled true if the genotype is ./.

and still doesn't distinguish partial no-calls.

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

So are you saying we should get rid of GenotypeType? I would generally agree.

@fnothaft

fnothaft Nov 14, 2016

Member

So are you saying we should get rid of GenotypeType? I would generally agree.

This comment has been minimized.

@heuermh

heuermh Nov 14, 2016

Member

As is, yeah. If these flags (or even extended ones as in Hail) turn out to be useful, then perhaps they could be added to the schema as flags instead of an enum.

@heuermh

heuermh Nov 14, 2016

Member

As is, yeah. If these flags (or even extended ones as in Hail) turn out to be useful, then perhaps they could be added to the schema as flags instead of an enum.

This comment has been minimized.

@fnothaft

fnothaft Nov 14, 2016

Member

SGTM

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Nov 15, 2016

Member

Rebased. @heuermh can you review and see if there are any changes needed? As far as I can tell, we are good to go.

Member

fnothaft commented Nov 15, 2016

Rebased. @heuermh can you review and see if there are any changes needed? As far as I can tell, we are good to go.

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 15, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 15, 2016

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1609/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains b68d8c0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision b68d8c0 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f b68d8c01403f41aa5ffe2a99c0ea89446166e21dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1609/

Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git -c core.askpass=true fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1263/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains b68d8c0 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1263/merge^{commit} # timeout=10Checking out Revision b68d8c0 (origin/pr/1263/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f b68d8c01403f41aa5ffe2a99c0ea89446166e21dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.

fnothaft added a commit to fnothaft/adam that referenced this pull request Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.

fnothaft added some commits Nov 12, 2016

Clean up `org.bdgenomics.adam.rich` package.
* Added scaladoc to all classes/methods that were missing docs.
* Deprecated `ReferenceSequenceContext`
* Deprecated implicit conversions to/from `RichAlignmentRecord` and eliminated
  dead code.
* Made `RichCigar` package private to `org.bdgenomics.adam`. It is only used
  in `org.bdgenomics.algorithms.consensus`. I considered moving it over, but
  decided to keep all "enriched" classes in `org.bdgenomics.adam.rich`. I did
  eliminate the `RichCigar` singleton and make `RichCigar` a case class, while
  moving the only non-`apply` method over to
  `org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator` as a private
  method.
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Nov 16, 2016

Member

Rebased and fixed conflicts and compile issue.

Member

fnothaft commented Nov 16, 2016

Rebased and fixed conflicts and compile issue.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Nov 16, 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/1613/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1613/
Test PASSed.

@heuermh heuermh merged commit f5cd15e into bigdatagenomics:master Nov 16, 2016

1 check passed

default Merged build finished.
Details
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Nov 16, 2016

Member

Thank you, @fnothaft!

Member

heuermh commented Nov 16, 2016

Thank you, @fnothaft!

heuermh added a commit that referenced this pull request Nov 16, 2016

[ADAM-1083] Cleaning up `org.bdgenomics.adam.models`.
Along with #1263 and #1264, this resolves #1083.

* Removing unused org.bdgenomics.adam.models.ReadBucket class.
* Move org.bdgenomics.adam.models.ReferencePositionPair and
  org.bdgenomics.adam.models.SingleReadBucket in to org.bdgenomics.adam.rdd.read
  and make package private.
* Clean up duplicated methods and methods that were incorrectly in companion
  singleton for SequenceDictionary and ReadGroupDictionary.
* Removed all SamReader references.
* Make writable file headers private to ADAM.
* Eliminated manual VCF parsing code in SnpTable.
* Cleaned up scaladoc for all classes and singleton objects.
* Moved `NonoverlappingRegions` test code out of `InnerBroadcastRegionJoinSuite`.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment