+ /**
+ * Scans the list of {@code ranges} for any values (positions) that lie
+ * between start and end (inclusive), and records the <em>offsets</em> from
+ * the start of the list as a BitSet. The offset positions are converted to
+ * corresponding words in blocks of {@code wordLength2}.
+ *
+ * <pre>
+ * For example:
+ * 1:1 (e.g. gene to CDS):
+ * ranges { [10-20], [31-40] }, wordLengthFrom = wordLength 2 = 1
+ * for start = 1, end = 9, returns a BitSet with no bits set
+ * for start = 1, end = 11, returns a BitSet with bits 0-1 set
+ * for start = 15, end = 35, returns a BitSet with bits 5-15 set
+ * 1:3 (peptide to codon):
+ * ranges { [1-200] }, wordLengthFrom = 1, wordLength 2 = 3
+ * for start = 9, end = 9, returns a BitSet with bits 24-26 set
+ * 3:1 (codon to peptide):
+ * ranges { [101-150], [171-180] }, wordLengthFrom = 3, wordLength 2 = 1
+ * for start = 101, end = 102 (partial first codon), returns a BitSet with bit 0 set
+ * for start = 150, end = 171 (partial 17th codon), returns a BitSet with bit 16 set
+ * 3:1 (circular DNA to peptide):
+ * ranges { [101-150], [21-30] }, wordLengthFrom = 3, wordLength 2 = 1
+ * for start = 24, end = 40 (spans codons 18-20), returns a BitSet with bits 17-19 set
+ * </pre>
+ *
+ * @param start
+ * @param end
+ * @param sourceRange
+ * @param sourceWordLength
+ * @param targetWordLength
+ * @return
+ */
+ protected final static BitSet getMappedOffsetsForPositions(int start,
+ int end, List<int[]> sourceRange, int sourceWordLength,
+ int targetWordLength)
+ {
+ BitSet overlaps = new BitSet();
+ int offset = 0;
+ final int s1 = sourceRange.size();