resetDB in VariantReviewTest on tearDown
Add support for loading bams (and other file types) via URLs with parameters.  The URL "path" is now used to determine file type, rather than the entire url string.  Also moved file type determination code to ResourceLocator class.
Merge remote-tracking branch 'origin/master'
Fix NPE in ResourceLocator
Minor code cleanup

Refactor getting alignment counts, check start/end in getValueString
Add ConsensusCalculator framework, basic implementation, and tests

No UI implementation yet

IGV-1961
Move IUPAC code table to util/resources

And parsing code to ParsingUtils
IGV-1962  Multiple "view mate region in split screen" operations fail.
Log errors better in ParsingUtils.loadMap
Initialize filteredSpliceJunctionFeatures as null

This was causing a bug where the filtering was not being performed because we were testing for null but it was actually a size 0 list
Formatting and whitespace changes only
Set showSashimi to be true
Merge pull request #53 from joshuagould/master

Show genomic location in tooltip
Add quick code for checking BCF files
Update javadoc for Plugin Feature interfaces
Add basic command line gatk_plugin

Still a long way from done, starting with UnifiedGenotyper
Add basic command line gatk_plugin

Still a long way from done, starting with UnifiedGenotyper
Update SamIndexerTest so it actually runs
Add method for creating BAM index to SamIndexer

Should probably reorganize this but we really just are calling through to Picard. Added unit test as well
Update VCFWriterTest to properly use vcf classes