Merge pull request #1 from amplab/master

pull in julie's latest changes
Initial version of Java VCF parser
Some refactoring
Merge pull request #2 from amplab/master

off by one error in writing normalize variants
Added smash4j command-line entry point.
Merge branch 'master' of https://github.com/kwestbrooks/smash
Reorganize code into multi-module project
Update .gitignore with ignoring target directories
Update .gitignore with IntelliJ files
Centralize version definition to parent POM
Remove trailing newlines
Added google-api-services-genomics client temporarily until it is available in maven central repo
Refactor dependencies across projects
Refactoring pom.xml files
Added GenomicsFactory for connecting to Google Cloud Genomics.
Merge pull request #3 from amplab/master

don't check allele match when evaluating SVs at exact breakpoint
Merge pull request #4 from amplab/master

clearer error message for variant pos collisions
Fetch Genomics API from Maven Central Repository!
Merge branch 'master' of https://github.com/kwestbrooks/smash
Added VariantFetcher to pull variants from Google Cloud Genomics