Correct seq position

[YuWei-CH]

1. Correct single-line annotation by modify start to start(l[3]) to 1 and end(l[4]) to length of seq.
2. Tested, by modifying testcase1 and 7 to have incorrect start and end times you still get correct results.
3. Handling of multiple-line annotations by:

• Step1: extract all start and end into corresponding set()
• Step2: Find min start and max end
• Step3: Check sequence length, validness of min_start and max_end
• Step4: Adjust start and end. Offset will be 0 if no adjust need
• Step5: Correct start(l[3]) and end(l[4]) by minus offset