added more debugging infomation

I can see a bug, but I do not know where it comes from.
dev-457: separated interval collection and seeding
dev-458: simplified the smem iterator

simpler but less powful.
dev-459: don't hard code the drop ratio

In the old code, if a secondary alignment is 50% worse, it won't be outputted.
dev-460: disallow a cigar 20M2D2I30M in extension

Global alignment does not allow contiguous insertions and deletions, but local
alignment and extension allow such CIGARs. The optimal global alignment may
have a lower score than extension, which actually happens often for PacBio
data. This commit disallows a CIGAR like 20M2D2I30M to fix this inconsistency.
Local alignment has not been changed.
dev-461: added a heuristic for PacBio data

See the comment above mem_test_chain_sw() for details.
dev-r462: refined setting for PacBio; weight flt

The recommended setting in the last commit is wrong. If we can extend a random
seed hit to the full length, we will force the read aligned through break
points, which is wrong. The new setting is better but it may lead to a small
fraction of fragmented alignments.

In addition, I added a filter on the minimum chain weight and tied
min_HSP_score to this filter. It doubles the mapping speed.
dev-463: added option -x to change multiple params

I hate to copy-paste long command line options.
Merge branch 'master' into mem