Added clarifying note to ADAMVariantContext

[laserson]

Not to be confused with ADAMVariationContext.

This is probably not the right place to put this note. Where should it go?

[fnothaft]

+1, good call!

[fnothaft]

BTW, I think that is an OK place to put the note, but I would wrap it in JAVADOC style comments (/*.../) so that it gets rendered as part of the Scaladoc for the API. Alternatively, you could add it as:

/**
 * @see org.bdgenomics.adam.rdd.variation.ADAMVariationContext This class is related to...
 */

[AmplabJenkins]

Can one of the admins verify this patch?

[fnothaft]

Jenkins, add to whitelist and test this please.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/21/

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/23/

[heuermh]

I would be in favor of renaming org.bdgenomics.adam.models.ADAMVariantContext to something else entirely.

[tdanford]

+1 on Michael's comment -- we had talked a while ago about renaming ADAMRecord too, I don't think there's any reason to stick to a naming scheme which matches GATK or Picard.

[fnothaft]

I actually don't think we need the ADAMVariantContext anymore anyways; it was useful with the original flat variant and genotypes schema that we had, but is no longer necessary with the current nested genotype schema.

@arahuja @timodonnel would dropping the ADAMVariantContext cause problems for guacamole?

[massie]

+1 on removing it if it's not needed. @arahuja @timodonnel?

[massie]

Jenkins, test this please.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/40/

[massie]

Jenkins test this please

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/46/

[tdanford]

No word from Arun or Tim -- why don't we merge this, and open a discussion issue for removing ADAMVariantContext. All in favor?

[tdanford]

Unless there are objections, Uri if you rebase this I will merge it.

[fnothaft]

@tdanford +1, we should do the discussion on the list anyways.

[laserson]

Rebased.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/50/

[fnothaft]

Merged! Thanks @laserson!