samtools/bcftools — pull request #21 by sm15 (2013-12-06 16:15:12+00:00)
Title: add new options to vcfview to select/exclude phased sites

option -p/P added to vcfview to select/exclude sites where all
samples are phased.

function bcf_all_phased returns true if all samples are phased.
haploid genotypes are considered phased, ./. => not phased,
.|. => phased, 0/1|2 => phased

tests added for these options. added a few sites to the view.vcf
test data so that the options could do something useful in the
test. updated output of other tests to reflect this too.