R CoverageRDD collapse method was misnamed.

bigdatagenomics · Aug 2, 2017 · ca3c587 · ca3c587
1 parent 544f78e
commit ca3c587
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/adam-r/bdg.adam/R/generics.R b/adam-r/bdg.adam/R/generics.R
@@ -158,6 +158,11 @@ setGeneric("realignIndels",
 
 #### Coverage operations ####
 
+# @rdname CoverageRDD
+# @export
+setGeneric("collapse",
+           function(ardd, ...) { standardGeneric("collapse") })
+
 # @rdname CoverageRDD
 # @export
 setGeneric("toFeatureRDD",

diff --git a/adam-r/bdg.adam/R/rdd.R b/adam-r/bdg.adam/R/rdd.R
@@ -574,7 +574,7 @@ setMethod("save",
 #' @return An RDD with merged tuples of adjacent sites with same coverage.
 #'
 #' @export
-setMethod("save", signature(ardd = "CoverageRDD"),
+setMethod("collapse", signature(ardd = "CoverageRDD"),
           function(ardd) {
               CoverageRDD(sparkR.callJMethod(ardd@jrdd, "collapse"))
           })