added VCF file creation and BAM file finding

added function allowing creation of VCF files from a list of BAM
files (found from supply of a base directory) to feed into the
VCF analysis functions later
added gzip check and unpacking function

The biggest cause of failed (hanging) runs was that the fastq
files were still zipped. So the script now checks to ensure that
all files it finds are unzipped, and if they are not, will use
gunzip to uncompress them. Should lead to fewer headaches in the
future.