First commit of Ketchup
Added additional filter option. Fixed bug in controlHomozygousFilter.
Edits to make build script compatible with Java 1.7
Finalizing the VCFComparator
Mods from Alex W to support java 1.7
More mods to VCFComparator and the VCFParser.
Ant script should now work outside the eclipse environment
More mods to vcf classes and a new app for benchmarking vcf files.
Dummy placeholder, will fix later.
More mods and options for vcf manipulation.
