New API for BGZF indexing w.r.t uncompressed data. Extended BGZF to read uncompressed files. Moved from RAZF to BGZF in FAI indexing.
bgzf.c: Check return status of bgzf_read_block in bgzf_useek to catch gzipped (as opposed to bgzipped) files.
Update khash.h from upstream sources

Attractivechaos/klib's 0.2.8 version includes quadratic probing.
Update kstring.[ch] from upstream sources

This attractivechaos/klib version includes error checking for memory
allocation and bug fixes for kputw(INT_MIN) and kputl(LONG_MIN).
Bug fix to handle blank headers in SAM files

Ensure str.s is an empty string rather than NULL, as it would be when
nothing has been added to it (e.g. as there were no headers at all).
Bug fix to stop sam view from converting 'H' into 'Z' types.
Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
Use strtoul() for other unsigned 'B' types too

Also reiterate why there's no byte swapping here, for new readers.
constify input parameter to faidx_fetch_seq
Use config.h for configuration options

Add the rudiments of a configuration header for _USE_KNETFILE,
BGZF_MT, and BGZF_CACHE instead of needing a special rule for bgzf.o.

Use it also in faidx.c, which had lost its _USE_KNETFILE define in htslib
and so lost its net functionality.  Also restore mistakenly removed #include
in faidx.c.

Fix makefile thinko: .pico files need prerequisites too.  Also fix
dependencies that were not updated with recent bgzf.c and faidx.c changes.
Replace HTS_VERSION with hts_version()

Provide a function returning the htslib version number, as the
interesting version number for user code is that of the library
it is running against, rather than the one it was built against.

Burning the version number into the library object (rather than some
arrangement of headers and #defines) also facilitates replacing the
version number coded into the Makefile with a Git description of the
working tree where appropriate.  This is done with GNU Make-specific
methods that don't interfere with "make: Nothing to be done for 'all'"
when nothing has changed.
Actually $(NUMERIC_VERSION) is more generic
[hts_open,bgzf,vcf] New flags for uncompressed input/output to distinguish between compressed/uncompressed BCF/VCF. Updates and fixes in BCF update functions. Removed old tests (now in samtools/bcftools repo) and added new.
Resolved merge conflict in Makefile, merged.
vcf.h: Reverted back to bcf_float_is_* macros as the inlined unions break vcfmerge code, found a solution with the original version.
Fix union-based type-punning buglet

Revert to union-based bcf_float_is_* macros with defined semantics, as
the issue here is about incorrect optimised code not just GCC warnings.

(The previous union initialiser initialised the wrong member of u.
This explicitly sets the desired float member.)
Use static inline, not just inline

Declare these as static inline in the C99-approved way, except for
bcf_gt_type() which shouldn't be inline at all.  Fixes issue #15.
Keep the makefile non-recursive

Write out prerequisites for test/test-vcf-api* (and add the executable
to .gitignore) so make can keep it up to date correctly.

Recursive makefiles are to be avoided because it's just not feasible to
get dependencies correct with them.  HTSlib now has correct dependency
information in its makefile, and it will be helpful to keep it that way.
Add faidx (FASTA index) description man page
vcf.h: New bcf_get_info_* and bcf_get_format_* calls