Output soft clipping for new cigar format too.

The new cigar format was introduced in
18cb19f692dc24ff84fed31e8e35e150e3c55599.
It distinguishes between a match ('=') and a mismatch('X') instead
of simply outputting 'M'.
But it lacked output of soft clipping.
Fix this by coping a part of ConvertAlignment() into
CalculateNumberMismatch().

Example cigar strings:
old (before 18cb):             9S13M1S
new (after 18cb):              1X1=1X3=1X1=1X2=2X
new fixed (after this change): 9S1X1=1X3=1X1=1X2=2X1S

old (before 18cb):             122S14M36S
new (after 18cb):              3=1X2=1X2=3X1=1X
new fixed (after this change): 122S3=1X2=1X2=3X1=1X36S