new vcfToMatrix format: tall and skinny
varscan is default; worked out a bug with it
level of depth and alt count are now in the output
figures out the allele appropriately through the GT info field
names the sample appropriately in the VCF output
file to convert SNP matrix from bcftools query into an MSA
can now create an MSA from bcftools
fixed a couple of bugs
fixed some wording
fixed the sample in the output file