Fix warnings about types passed to abs() functions

[leecbaker]

Use different versions of abs() based on the data types passed to them.

Fixes warnings when building with clang on OS X.

Warnings are similar to:

bwa.c:147:18: warning: absolute value function 'abs' given an argument of type
      'long long' but has parameter of type 'int' which may cause truncation of
      value [-Wabsolute-value]
                w = (max_gap + abs(rlen - l_query) + 1) >> 1;
                               ^
bwa.c:147:18: note: use function 'llabs' instead
                w = (max_gap + abs(rlen - l_query) + 1) >> 1;
                               ^~~
                               llabs

[jmarshall]

But w and min_w are ints…

[leecbaker]

Updated the PR to truncate the int64_t parameters to int before doing the abs(). I think this should address concerns about the return type.