VCFFileReader:
Added functionality so that fromVCF can create an intervalList with or without filtered variants (defaulting to without, as currently)
Added functionality to fromVCF so that the intervals will end at the END value from the info field (if available).
Merge pull request #132 from samtools/yf_include_filtered_variants__when_creating_intervallist

VCFFileReader added functionality to .fromVCF