Port fixes from samtools razf.c/h to htslib.
vcfcheck: More readable output, replace "-" by "<STDIN>" when reading from standard input
Revert to kstring.h with a separate kstring.c

Revert to our kstring.c/.h prior to 18ac8061fbf174784b8f169523adab2cd5226b17
which, having a separate C file, is more similar to the kstring in samtools
and klib.
Fix <stdarg.h> include

As we no longer get this by accident from kstring.h, include it ourselves.
Merge changes from samtools's kstring

Adds kputl() and a bug fix for kputw(INT_MIN).  This kstring.h is now the
same as the current samtools one, but with kputc_() and kputsn_() added.

(The same bug exists in this kputl(LONG_MIN), so that function will need
fixing or reimplementing in due course.)
vcfview: Fix in bcf_subset; force unpacking on VCF output
tbx: Allow indexing of empty files, do not segfault
vcfutils: bcf_gt_type should not be declared as static
vcf.[hc]: API to update FILTER column. BCF output not supported yet in this version
vcfmerge, vcfnorm: Append command and version string to VCF header
vcffilter &friends: Filtering of indels now supported. Changes in vcfcheck, plot-vcfcheck and vcfquery to reflect that. More changes and fixes to come, but this version seems stable and fully functional.
Updated tests
Replace with samtools's ksort

We previously had a stripped-down ksort.h; this re-adds the other
sorts alongside introsort and fixes a non-static inline.

This ksort.h is now identical to the current samtools one.
vcfcheck: Changed output format of Ts/Tv
vcffilter,gtcheck: Added sanity checks; Extended help message; Changed the order of columns on gtcheck output
plot-vcfcheck: Produce the overlap by AF graphs
Add klist.h, as used by samtools

This is upstream klib's klist.h, which differs from samtools's
previous version only in copyright boilerplate and include guard.
synced read and vcftools: Changed the -f, --apply-filters switch so that it accepts a list of allowed FILTERs. This is useful for example in cases when PASS has to be distinguished from "."
Maintain the same API regardless of -D BGZF_MT

As is done for BGZF_CACHE, bgzf.h should expose the same ABI (both
API function and structure layout) regardless of whether BGZF_MT
is defined.
vcffilter: FILTER column of hard-filtered sites now lists failed filters; Unset the FILTER of skipped sites only with -u switch, not by default.