initial commit.
added a template VCF file for PyVCF.
defined missing template vcf filename.
documented required args for _Record.
added comments and missing value for _Record.
defined empty entries adding info to the list of fields not to population from the tab-delimited file.
use named index values and convert alt allele to a list per PyVCF's weird parsing in the _Record constructor.
removed samples and other extraneous data from the template.
simplified template to absolute minimum required by seattleseq.
added argument for reference file.
added functions to convert GATK indels to VCF indels and fetch sequences from a given reference file.
calculate variant size.
removed variant size from the gatk indel function.
finished logic for correcting ref/alt bases based on whether the event was an insertion or a deletion.
convert gatk indels to vcf style indels.
don't assume anything about the reference fasta.
added doctests for a deletion and a large insertion.
added requirements for pip.
replaced biopython with fastahack.
replaced UCSC doctest reference with 1KG reference.