fix NAMESPACE, doc warnings

bigdatagenomics · Sep 6, 2017 · a2d3e5c · a2d3e5c · pbashyal-nmdp · Sep 6, 2017
1 parent 3e06868
commit a2d3e5c
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Showing 2 changed files with 19 additions and 1 deletion.
diff --git a/adam-r/bdg.adam/NAMESPACE b/adam-r/bdg.adam/NAMESPACE
@@ -6,28 +6,42 @@ exportClasses(AlignmentRecordRDD)
 exportClasses(CoverageRDD)
 exportClasses(FeatureRDD)
 exportClasses(FragmentRDD)
+exportClasses(GenomicDataset)
+exportClasses(GenomicRDD)
 exportClasses(GenotypeRDD)
 exportClasses(NucleotideContigFragmentRDD)
+exportClasses(VariantContextRDD)
 exportClasses(VariantRDD)
 exportMethods(aggregatedCoverage)
+exportMethods(collapse)
 exportMethods(countKmers)
 exportMethods(coverage)
 exportMethods(flankAdjacentFragments)
 exportMethods(flatten)
 exportMethods(loadAlignments)
 exportMethods(loadContigFragments)
+exportMethods(loadCoverage)
 exportMethods(loadFeatures)
 exportMethods(loadFragments)
 exportMethods(loadGenotypes)
 exportMethods(loadVariants)
 exportMethods(markDuplicates)
+exportMethods(pipe)
 exportMethods(realignIndels)
 exportMethods(recalibrateBaseQualities)
 exportMethods(save)
+exportMethods(saveAsParquet)
+exportMethods(saveAsSam)
+exportMethods(saveAsVcf)
+exportMethods(sort)
+exportMethods(sortLexicographically)
 exportMethods(sortReadsByReferencePosition)
 exportMethods(sortReadsByReferencePositionAndIndex)
 exportMethods(toCoverage)
 exportMethods(toDF)
-exportMethods(toFeatureRDD)
+exportMethods(toFeatures)
 exportMethods(toFragments)
 exportMethods(toReads)
+exportMethods(toVariantContexts)
+exportMethods(transform)
+exportMethods(transmute)
diff --git a/adam-r/bdg.adam/R/rdd.R b/adam-r/bdg.adam/R/rdd.R
@@ -748,6 +748,8 @@ setMethod("saveAsParquet", signature(ardd = "GenotypeRDD", filePath = "character
               invisible(sparkR.callJMethod(ardd@jrdd, "saveAsParquet", filePath))
           })
 
+#' Converts this RDD of Genotypes to VariantContexts.
+#'
 #' @return Returns this RDD of Genotypes as VariantContexts.
 #'
 #' @export
@@ -825,6 +827,8 @@ setMethod("saveAsParquet", signature(ardd = "VariantRDD", filePath = "character"
               invisible(sparkR.callJMethod(ardd@jrdd, "saveAsParquet", filePath))
           })
 
+#' Converts this RDD of Variants to VariantContexts.
+#'
 #' @return Returns this RDD of Variants as VariantContexts.
 #'
 #' @export