Add SAM and VCF man pages extracted from samtools.1

We're splitting up samtools's samtools.1 man page into separate samtools
and bcftools man pages, and small separate pages summarizing the formats.
Add BAM_FSUPPLEMENTARY flag bit

Consideration was given to adding this flag to BAM_DEF_MASK, so that
supplementary alignments would not appear in bam_plp_init() pileups
by default.  However unlike secondary alignments, these in fact probably
should appear by default; they can be suppressed via bam_plp_set_mask().
Get rid of %ld compilaiton warnings
Return bytes >= 0x80 from hgetc() correctly
Fixed CRAM to code with the 0x800 supplementary flag.
Merge pull request #27 from jkbonfield/develop

Fixed CRAM to code with the 0x800 supplementary flag.
vcf: New bcf_hdr_printf() call
Merge branch 'bcftools+calling' into develop