+ return covers(seq, false, false);
+ }
+
+ /**
+ *
+ * @param seq
+ * @param localCover
+ * - when true - compare extent of seq's dataset sequence rather
+ * than the local extent
+ * @param either
+ * - when true coverage is required for either seq or the mapped
+ * sequence
+ * @return true if mapping covers full length of given sequence (or the
+ * other if either==true)
+ */
+ public boolean covers(SequenceI seq, boolean localCover, boolean either)
+ {
+ List<int[]> mappedRanges = null, otherRanges = null;