CLI component changes for new variant schema #100
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…Vcf, and remove the implementation of ComputeVariants
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One or more automated tests failed |
| * @return GATK Variant context post conversion. | ||
| */ | ||
| def convert(vc: ADAMVariantContext): VariantContext = { | ||
| val variant: ADAMVariant = ADAMVariant.newBuilder |
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The diff is a little screwy here—this is the body of the convert(VariantContext): ADAMVariantContext/ADAMVariant method, correct?
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Definitely. On Thu, Feb 13, 2014 at 1:18 PM, Frank Austin Nothaft <
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| @@ -28,7 +28,9 @@ object AdamMain extends Logging { | |||
| PileupAggregator, | |||
| ListDict, | |||
| CompareAdam, | |||
| ComputeVariants, | |||
| /* TODO (nealsid): Reimplement in terms of new schema | |||
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Will this show up in a later PR?
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Yes! Or I can remove it if it's going to be replaced by your variant
calling work in the future.
On Fri, Feb 14, 2014 at 4:10 PM, Frank Austin Nothaft <
notifications@github.com> wrote:
In adam-cli/src/main/scala/edu/berkeley/cs/amplab/adam/cli/AdamMain.scala:
@@ -28,7 +28,9 @@ object AdamMain extends Logging {
PileupAggregator,
ListDict,
CompareAdam,
- ComputeVariants,
- /* TODO (nealsid): Reimplement in terms of new schema
Will this show up in a later PR?
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Reply to this email directly or view it on GitHubhttps://github.com//pull/100/files#r9764053
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Nah! Just wanted to check.
Is it still necessary with the new schema? IIRC, in the current system, this is used for generating variants from genotypes; I'm not sure if this transformation makes sense with the new schema.
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Jenkins, test this please. |
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It is OK from my end. |
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One or more automated tests failed |
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@nealsid If you confirm that the failing test is expected, I'll go ahead and merge this. Looking forward to your follow-on work. |
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@massie Thanks, these are expected. |
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Thanks, Neal! |
CLI component changes for new variant schema
As in the other pull requests, this is a superset of the other commits and should decrease in size once those are merged. The commits meant to be reviewed in this PR are limited to the CLI changes for the new variant schema & changes.
Thanks!
Neal