Merge branch 'develop' into bcftools+calling
sam: New bam_str2flag and bam_flag2str functions for a more user-friendly setting of bitmasks. Removed the default pileup filters (except for BAM_FUNMAP) and moved the filtering to BAM-reading callbacks
Merge branch 'bcftools+calling' into develop
Merge branch 'develop' into bcftools+calling
Merge branch 'bcftools+calling' into develop
faidx: Detect compressed BGZF fasta files and create .gzi index without asking to allow proper functioning of samtools faidx fasta.fa.gz
synced_reader: Improved regions/targets to be faster with large number of sequences; More userfriendly regions_overlap() function
vcf: bcf_update_format now sets the number of samples in VCF record which previously was responsibility of the user; Fix in bcf_itr_querys macro, non-existent bcf_name2id renamed to bcf_hdr_name2id
Migrate documentation from samtools bam.h to sam.h and add a few more items.
Add Copyright notice.