add .listCumsumShifted() helper back

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@96942 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Nov 20, 2014 · 584c39a · 584c39a
1 parent ce2c973
commit 584c39a
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,7 +7,7 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representing and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.19.12
+Version: 1.19.13
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,

diff --git a/R/mapCoords-methods.R b/R/mapCoords-methods.R
@@ -27,6 +27,13 @@
     res
 }
 
+.listCumsumShifted <- function(x) {
+  cs <- unlist(cumsum(x), use.names=FALSE)
+  shifted <- c(0L, head(cs, -1))
+  shifted[start(PartitioningByWidth(elementLengths(x)))] <- 0L
+  shifted
+}
+
 .mapCoords <- function(from, to, ..., ignore.strand, elt.hits, p=FALSE) {
     if (ignore.strand)
         strand(to) <- "*"
@@ -57,9 +64,7 @@
                                   width=width(eltPosition)[neg])
     }
     ## location wrt start of combined list elements (e.g., transcript-level)
-    cs <- unlist(cumsum(width(to)), use.names=FALSE)
-    shifted <- c(0L, head(cs, -1))
-    shifted[start(PartitioningByWidth(elementLengths(to)))] <- 0L
+    shifted <- .listCumsumShifted(width(to))
     cumPosition <- shift(eltPosition, 1L + shifted[sHits])
 
     toInd <- togroup(to)[sHits]