manpage: Described ordering of chroms with -r and -t
mcall: Replacement of zero QS(ref) now based on nSamples and avgDP.
add tests to which output bcf and compare with outputing vcf

- add tests, where appropriate, to output bcf and compare with outputing vcf
- remove version specific cruft from test outputs
- reveals probelms with norm and concat, so some tests failing
isec: Capture -p,-w usage mistakes
isec: Allow -w with Venn-like subsets
travis: Use --branch=develop for htslib
annotate: Fix in initialization when -a is VCF/BCF
call: Basic support for gVCF
Merge branch 'develop' of github.com:samtools/bcftools into develop
annotate: Allow editing of FILTER columns as well
Updated documentation and tests
gvcf: Interrupt gVCF blocks on missing sites
view: Exit nicely on hts_open failure
Added missing test files
view --trim-alt-alleles: Check return status of bcf_trim_alleles
Disabled test of annotate plugins as it requires libhts.so
annotate: Give usage hint if either one of -l or -p fail
annotate: Fix error message typos
annotate: When annotating from VCFs *some* alleles must match, not *all*
man page: Clarified usage of `annotate -p`