synced_reader: Added support for alleles in targets files to select best matching line out of possibly duplicate VCF records.
vcf: Added bcf_get_variant_type[s]() call to avoid the need for explicit call of bcf_set_variant_types(); The mpileup's X allele is not a SNP; Get rid of htfile warnings
Proper initialization in hts_readlines
bcf_index_build: Check if the BCF is compressed
Fixed a rather surprising bug in CSI index access via hts_itr_next, before it was not possible to obtain BCF record at chr:pos-pos. The fix may have unexpected consequences in other situations and file formats, beware!
vcf.c: Proper freeing of memory taken by dirty info/fmt tags when update routine called multiple times
New feature in bcf_synced_reader: negate the sample selection in bcf_sr_set_samples by exclamation mark
vcf.h: Add out of range check into bcf_idinfo_exists() as it always has to be checked elsewhere.
vcf.h: New API call: bcf_get_genotypes()
vcf.c: Call bcf_unpack() on user's behalf in all bcf1_get/update routines
synced_reader: Fixed an off by one error in bcf_sr_next_line() to properly match target alleles
vcf: Tidied up vcf.h, made API more consistent and extended documentation
vcf module: Made the naming more consistent to avoid confusion about which of the vcf/bcf_* function variant to use.
Merge branch 'bcftools+calling' into develop
Merge branch 'develop' of github.com:samtools/htslib into develop
hfile: Removed accidently commited local change in blksize