bcftools view: Output CLR,UGT,CGT tags in -m pair/trio calling. In this version, consistency with output genotypes is not being checked.
bcftools view: prevent segfault when running in plain mode, p1 then does not exist
bcftools view: previous fix in kt_fisher_exact (PV4 annotations, fet.c) was wrong. Will this one work better?
bam_pileup: Improved read pair overlaps clipping. Disabled for now as more testing is needed.
Merge branch 'develop' of github.com:samtools/samtools into develop