Vcf work remove old variant #98
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| @@ -30,521 +31,66 @@ import fi.tkk.ics.hadoop.bam.VariantContextWritable | |||
| * If an annotation has a corresponding set of fields in the VCF standard, a conversion to/from the | |||
| * GATK VariantContext should be implemented in this class. | |||
| */ | |||
| class VariantContextConverter extends Serializable { | |||
| private[adam] class VariantContextConverter extends Serializable with Logging { | |||
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RE: making this class private to ADAM, I think that this is a good idea, but would note one downstream concern: it is useful to expose a method for converting an RDD of GATK VariantContexts to an RDD of AdamVariants. People who are building tools downstream may need to do this conversion—the big use case is if you have to open a pipe to/from an application that needs VCF. It'd probably be best to expose that via AdamRDDFunctions.
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Neal—do you want me to merge #97 to clean up these diffs? |
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Sure. On Thu, Feb 13, 2014 at 1:10 PM, Frank Austin Nothaft <
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Thanks for the updates Neal! I am going to hold off on merging this PR through tomorrow, so that more people may review the code. If no more issues are raised by tomorrow afternoon, I will merge the request. |
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Thanks, Frank. Let me know if there's anything else blocking this. |
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Looks good to me—will just wait until noon to merge in case anyone else wants to review the code; then I'll move on to #100 . |
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Thanks @nealsid ! I've just merged this PR. |
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Thanks, Frank! On Fri, Feb 14, 2014 at 4:07 PM, Frank Austin Nothaft <
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This pull request is against vcf-work but it has commits that are inside vcf-work-schema (the other outstanding PR). Once vcf-work-schema is merged this PR will be smaller and only contained unreviewed changes. Let me know if there's a cleaner way to send this so only diffs between this and vcf-work-schema are shown.