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
r807: allow to change block size in bwt_gen

For a very large reference genome, the default is too small.
r808: a minor bug with the new index -b
r809: new strategy for the -a mode
Add @HD tag to SAM header
Merge pull request #30 from mp15/header_hd

Add @HD tag to SAM header
r810: add err_puts()

puts() adds '\n', but fputs() does not.
wrong function to print @HD line in bwa_print_sam_hdr
Merge pull request #31 from jwbargsten/master

wrong function to print @HD line in bwa_print_sam_hdr
r815: optionally output ref fasta header

Also fixed a bug in reading .ann files