restore 'maxgap' special meaning when 'type' is set to "start" or "end"

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@104699 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -7,13 +7,13 @@ 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: 1.21.14
+Version: 1.21.15
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
 	GenomeAnnotation
 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.11.3), S4Vectors (>= 0.7.3),
-	IRanges (>= 2.3.9), GenomeInfoDb (>= 1.1.20)
+	IRanges (>= 2.3.11), GenomeInfoDb (>= 1.1.20)
 Imports: utils, stats, XVector
 LinkingTo: S4Vectors, IRanges
 Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>= 2.25.3),

R/findOverlaps-methods.R

@@ -142,10 +142,8 @@ findOverlaps_GenomicRanges <- function(query, subject,
              algorithm=c("nclist", "intervaltree"),
              ignore.strand=FALSE)
 {
-    min.score <- IRanges:::min_overlap_score(maxgap, minoverlap)
     type <- match.arg(type)
-    if (!identical(maxgap, 0L) && type != "any")
-        warning(IRanges:::maxgap_special_meaning_msg)
+    min.score <- IRanges:::min_overlap_score(maxgap, minoverlap, type)
     select <- match.arg(select)
     algorithm <- match.arg(algorithm)
     if (algorithm != "nclist")
@@ -586,10 +584,8 @@ countOverlaps_GenomicRanges <- function(query, subject,
               algorithm=c("nclist", "intervaltree"),
               ignore.strand=FALSE)
 {
-    min.score <- IRanges:::min_overlap_score(maxgap, minoverlap)
     type <- match.arg(type)
-    if (!identical(maxgap, 0L) && type != "any")
-        warning(IRanges:::maxgap_special_meaning_msg)
+    min.score <- IRanges:::min_overlap_score(maxgap, minoverlap, type)
     algorithm <- match.arg(algorithm)
     if (algorithm != "nclist")
         warning("'algorithm' is ignored when 'query' or 'subject' ",