fix poverlaps()

Author: lawremi

R/findOverlaps-methods.R

@@ -258,5 +258,5 @@ setMethod("poverlaps", c("GenomicRanges", "GenomicRanges"),
     seqnames(query) == seqnames(subject) &
         (if (ignore.strand) TRUE
          else compatibleStrand(strand(query), strand(subject))) &
-        poverlaps(ranges(query), ranges(subject), maxgap, minoverlaps, type)
+        poverlaps(ranges(query), ranges(subject), maxgap, minoverlap, type)
 })

inst/unitTests/test_findOverlaps-methods.R

@@ -318,3 +318,17 @@ test_findOverlaps_with_circular_sequences <- function()
     .checkHits(1:4, 1:4, 4, 4, current5, select="all")
 }
 
+test_poverlaps <- function() {
+    ans <- poverlaps(GRanges(), GRanges())
+    checkIdentical(ans, Rle())
+
+    ans <- poverlaps(GRanges("chr1:11-15"), GRanges("chr1:16-20"))
+    checkIdentical(ans, Rle(FALSE))
+
+    ans <- poverlaps(GRanges("chr1:11-16"), GRanges("chr1:16-20"))
+    checkIdentical(ans, Rle(TRUE))
+
+    ans <- poverlaps(GRanges(c("chr1:11-15", "chr1:11-16")),
+                     GRanges("chr1:16-20"))
+    checkIdentical(ans, Rle(c(FALSE, TRUE)))
+}