r377: increased unpaired penalty from 9 to 17

This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
r378: bugfix - wrong CIGAR

This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
r379: fixed compiling error
r380: er... another compiling error
r381: fixed a bug when upper bound < max read len
r382: similar treatment in bwa-sw (see r381)
Merge branch 'master' into master_fixes