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Implement contig-to-RefSeq translation, refactor SequenceDictionary with... #238

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mlinderm
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@mlinderm mlinderm commented May 5, 2014

... RefSeq information (and without numeric IDs) and prepare ADAMGenotype for incorporating reference model information.

This started as a series of small edits to ADAMVariant/ADAMGenotype, but then started sprawling… First part of addressing #158.

…ith RefSeq information (and without numeric IDs) and prepare ADAMGenotype for incorporating reference model information.
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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/316/

adamVariants.flatMap(p => p.genotypes).adamSave(args.outputPath,
blockSize = args.blockSize, pageSize = args.pageSize,

def getDictionaryFile(name: String): Option[File] = {
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This method is identical to the one in ADAM2Vcf. It probably makes sense to factor our getDictionary into a separate class that both use.

…omments in PR re: incorporation of RefSeq IDs into SequenceDictioanry
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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/319/

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All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/320/

import org.bdgenomics.adam.models.SequenceDictionary
import net.sf.samtools.SAMFileReader

trait DictionaryCommand {
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I like this trait. Good idea!

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massie commented May 12, 2014

Thanks, Michael! Love all the tests and clean code.

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massie commented May 12, 2014

Can you rebase this onto master? Once that's done, this is ready to merge.

@massie massie mentioned this pull request May 14, 2014
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massie commented May 14, 2014

@mlinderm I had a little time so I thought I'd save you the rebase suffering. I'll merge #243 when tests pass and close this request. Thanks for this work, Michael!

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3 participants