r787: use mem_seed_sw() also for non-PacBio reads

In the previous version, mem_seed_sw() is only used for PacBio reads to filter
bad seeds. For non-PacBio long queries, bwa-mem uses mem_chain2aln_short() for
a similar purpose. However, it turns out that mem_chain2aln_short() is not
effective given long near-tandem repeats. Bwa-mem still wastes a lot of time
of futile ref substring and extensions.

In this commit, mem_chain2aln_short() has been removed. mem_seed_sw() is used
if the query sequence is long enough (~700bp). For shorter reads, the results
should be almost identical to the previous version.
r788: segfault when the last ref is "weird"

mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
Released 0.7.10
adding support for SAM/BAM output using htslib.  Please turn on within
the Makefile.
don't process hard clipped SEQ

The full read sequence has to be present.
first integration; compiled, but NOT TESTED!
r795: intel's ksw_extend() replacement
r796: more debugging code
don't process hard clipped SEQ

The full read sequence has to be present.
Merge branch 'master' of github.com:lh3/bwa
Fixed a bug related to the score returned.
Merge branch 'master' into new-master
Merge branch 'nh_bam_support' of git://github.com/nh13/bwa into nh13-nh_bam_support
r806: polish BAM support
adding determinism to bwa mem by allowing the user to specify a fixed
chunk size, rather than have it vary due to the number of threads.