added clipping

[lskatz]

This is untested except that I know that there aren't syntax errors. Addresses #15

Adds --clip to remove any soft clipping and convert them to hard clipping

Examples (in theory):

• 174M76S gets converted to 174M76H and 76bp gets trimmed
• 174M10S10H gets converted to 174M20H and 10bp gets trimmed
• 10S174M gets converted to 10H174M, 10bp gets trimmed, and the position changes by 10bp

Reply in the conversation if you tested it rigorously or at all.

[misshie]

According to the SAM format specification, both "S" and "H" CIGAR operators are defined as "consumes reference == no." Therefore, the following two lines at the end of the clip function:

# update the position of the mapping according to how much we clipped from the left
$sam[SAM_POS] += $SL;

are likely unnecessary.