core vcf: added API for modifying/deleting/adding INFO fields, currently only VCF output supported; vcfmerge: AN,AC tags now updated correctly.
vcfcheck: Do not crash at non-variant sites. Restore checking of two VCFs.
VCF/BCF core lib: Allow missing values in vectors. Note that this is a major change which, in contrast to BCFv2.1 specification, allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators.  Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. This trial BCF version (v2.2) is compatible with the VCF specification and enables to handle correctly vectors with different ploidy in presence of missing values.
gtcheck: Removed forgotten debugging line
A few bugfixes from the previous two commits. New -S option in gtcheck and -H made work also in the cross-check mode
vcfquery fix: Allow a mask file with the -v option
vcfcheck: complain if tabix index not available with -t option
vcfcheck: Do not run in streaming mode with the -t option
vcffilter: fixed a typo, output file names now named correcly based on filter type
bcf1_update_info fix: initialize bcf_info_t pointer, do not pass NULL
vcffilter: extended help message
vcffilter: allow arbitrary order in -f and -l filtering options (X>value is same as value<X)
vcffilter: plot annotation distributions
vcfview: Restored the subset functionality
vcfview: Restored the subset functionality (continued)
vcfmerge: do not crash with non-overlapping chromosomes
vcffilter: Plot also cropped annotation distributions to show the range of values actually used in filtering
vcfgtcheck: Fix in INFO/DP parsing, wrong ID was used before
vcfmerge: fix of copy-and-paste error in format field merging, use correct integer ranges
gtcheck: fixed incorrect output, instead of uncertainty, the opposite (confidence) was reported before