@@ -2412,7 +2412,7 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

         sh <- max(0, min(h, .dpOrDefault(GdObject, "stackHeight", 0.75))) / 2

         boxOnly <- res > 10

         if (boxOnly) {

-            x <- c(start(readInfo), rep(end(readInfo), 2), start(readInfo))

+            x <- c(start(readInfo), rep(end(readInfo)+1, 2), start(readInfo))

             y <- c(rep(readInfo$stack + sh, 2), rep(readInfo$stack - sh, 2))

             id <- rep(readInfo$uid, 4)

         } else {

@@ -2426,20 +2426,20 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

             readInfo$arrow[match(names(arrowMap), readInfo$uid)] <- arrowMap

             ## The parts that don't need arrow heads

             sel <- is.na(readInfo$arrow) | readInfo$arrow == "*"

-            x <- c(start(readInfo)[sel], rep(end(readInfo)[sel], 2), start(readInfo)[sel])

+            x <- c(start(readInfo)[sel], rep(end(readInfo)[sel]+1, 2), start(readInfo)[sel])

             y <- c(rep(readInfo$stack[sel] + sh, 2), rep(readInfo$stack[sel] - sh, 2))

             id <- rep(readInfo$uid[sel], 4)

             ## The arrow heads facing right

             w <- Gviz:::.pxResolution(coord = "x", 5)

             sel <- readInfo$arrow == "+"

-            ah <- pmax(start(readInfo)[sel], end(readInfo)[sel] - w)

-            x <- c(x, start(readInfo)[sel], ah, end(readInfo)[sel], ah, start(readInfo)[sel])

+            ah <- pmax(start(readInfo)[sel], end(readInfo)[sel]+1 - w)

+            x <- c(x, start(readInfo)[sel], ah, end(readInfo)[sel]+1, ah, start(readInfo)[sel])

             y <- c(y, rep(readInfo$stack[sel] + sh, 2), readInfo$stack[sel], rep(readInfo$stack[sel] - sh, 2))

             id <- c(id, rep(readInfo$uid[sel], 5))

             ## The arrow heads facing left

             sel <- readInfo$arrow == "-"

             ah <- pmin(end(readInfo)[sel], start(readInfo)[sel] + w)

-            x <- c(x, start(readInfo)[sel], ah, rep(end(readInfo)[sel], 2), ah)

+            x <- c(x, start(readInfo)[sel], ah, rep(end(readInfo)[sel]+1, 2), ah)

             y <- c(y, readInfo$stack[sel], rep(readInfo$stack[sel] + sh, 2), rep(readInfo$stack[sel] - sh, 2))

             id <- c(id, rep(readInfo$uid[sel], 5))

         }

@@ -2463,7 +2463,7 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

             mateGaps <- mateGaps[start(rmap) <= start(mateGaps) & end(rmap) >= end(mateGaps)]

             gy <- readInfo$stack[match(as.character(seqnames(mateGaps)), readInfo$entityId)]

             lineCoords <- data.frame(

-                x1 = start(mateGaps) - 1, y1 = gy, x2 = end(mateGaps) + 1, y2 = gy,

+                x1 = start(mateGaps), y1 = gy, x2 = end(mateGaps) + 1, y2 = gy,

                 col = .dpOrDefault(GdObject, c("col.gap", "col"), .DEFAULT_SHADED_COL),

                 lwd = .dpOrDefault(GdObject, c("lwd.gap", "lwd"), 1),

                 lty = .dpOrDefault(GdObject, c("lty.gap", "lty"), 1),

@@ -2505,7 +2505,7 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

             gy <- readInfo$stack[match(names(delGaps), readInfo$entityId)]

             if (length(delGaps)) {

                 delCoords <- data.frame(

-                    x1 = start(delGaps) - 1, y1 = gy, x2 = end(delGaps) + 1, y2 = gy,

+                    x1 = start(delGaps)+1, y1 = gy, x2 = end(delGaps) + 1, y2 = gy,

                     col = .dpOrDefault(GdObject, c("col.deletion", "col"), .DEFAULT_BRIGHT_SHADED_COL),

                     lwd = .dpOrDefault(GdObject, c("lwd.deletion", "lwd"), 1),

                     lty = .dpOrDefault(GdObject, c("lty.deletion", "lty"), 1),

@@ -2625,6 +2625,7 @@ setMethod("drawGD", signature("AlignmentsTrack"), function(GdObject, minBase, ma

     }

     return(switch(as.character(exponent),

         "0" = sprintf("%i", as.integer(tckText)),

+        #"0" = sprintf("%s bp", tckText),

         "3" = sprintf("%s kb", tckText),

         "6" = sprintf("%s mb", tckText),

         "9" = sprintf("%s gb", tckText),