// we are comparing a sequence to its own subsequence (the group) + hidden
// columns.
- CigarArray cig = new CigarArray(al, hc, sg1);
+ // no hidden columns case
+ CigarArray cig = new CigarArray(al, null, sg1);
String result = cig.getCigarstring();
+ assertEquals(result, "22M");
+
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
assertEquals(result, "1M4D9M5D3M");
// group starts at hidden cols