Implement contig-to-RefSeq translation, refactor SequenceDictionary with... #238
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…ith RefSeq information (and without numeric IDs) and prepare ADAMGenotype for incorporating reference model information.
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All automated tests passed. |
| adamVariants.flatMap(p => p.genotypes).adamSave(args.outputPath, | ||
| blockSize = args.blockSize, pageSize = args.pageSize, | ||
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| 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. |
…equenceDictioanry
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All automated tests passed. |
| import org.bdgenomics.adam.models.SequenceDictionary | ||
| import net.sf.samtools.SAMFileReader | ||
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| trait DictionaryCommand { |
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Thanks, Michael! Love all the tests and clean code. |
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Can you rebase this onto master? Once that's done, this is ready to merge. |
This was referenced May 21, 2014
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... 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.