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
Migrate documentation from samtools bam.h to sam.h and add a few more items.
Add Copyright notice.