bgzf: Write plain gzip files if is_gzip set
bgzf_open(..,"g") for compressed gzip output, as opposed to BGZF
Don't install libhts.so.1 as a man page
Release 1.1: various minor bug fixes
Merge version number bump from master
Added regidx API which should replace bcf_sr_regions at some point
Clean after regidx init failure; fixed build dependencies
Fix in bcf regions which in some situations would skip first

the first position on new chromosome in the loci list.
regidx: simple file format autodetection
add new test-regidx binary to .gitignore
Formatting fixes for man page

There is no .R; replace badly-nested .RE with .PP;
use hyphens to introduce options rather than en dashes
(addresses samtools/www.htslib.org#5 for tabix man page).
Merge pull request #136 from mcshane/feature/ignore_test-regidx

add new test-regidx binary to .gitignore
Return type of bgzf_getc is int, not char
regidx: use size_t, not ssize_t
Fix regidx.o dependencies and htslib.mk; alphabetise
Merge man page formatting fixes
Support for Type=Character, in htslib same as Type=String
VCF header editing speedup for large number of ref sequences

- Don't sync the internals with each edit, just set a 'dirty' flag and call
  bcf_hdr_sync() when header is written.  This may have undesired consequences
  in existing programs which do not call bcf_hdr_write() or try to access newly
  added fields before bcf_hdr_sync() was called.

- bcf_hdr_add_sample() does not require NULL any more, but programs may
  continue calling it for backward compatibility.

Resolves https://github.com/samtools/samtools/issues/308
New bcf_copy API
Remove -DSAMTOOLS vestiges

hclose() is always paranoid (it flushes, syncs, and reports errors),
and cram_FILE is now always hFILE.