- Modified VCF loading and annotation system to support insertions, deletions, in-dels.  Modified client where necessary to support these changes.
Fixed up some merge issues
Beginnings of MedSavant JSON client application
Changed JSON library to gson.
Added some missing files
Implementing speed tweaks for annotation. not yet buildable.
Still not working -- all annotations are null.  See VariantAnnotatorIOJob in BatchVariantAnnotator.
Working on indel support...
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Conflicts:
	MedSavantServerEngine/src/main/java/org/ut/biolab/medsavant/server/serverapi/AnnotationManager.java
Merge branch 'master' into indel
Progress on indel support
Cleaned up code in preparation for merge
Merge branch 'indel'

Conflicts:
	MedSavantClient/src/main/java/org/ut/biolab/medsavant/client/util/ExportVCF.java
	MedSavantClient/src/main/java/org/ut/biolab/medsavant/client/view/genetics/variantinfo/BasicVariantSubInspector.java
	MedSavantClient/src/main/java/org/ut/biolab/medsavant/client/view/genetics/variantinfo/DetailedVariantSubInspector.java
	MedSavantClient/src/main/java/org/ut/biolab/medsavant/client/view/genetics/variantinfo/SimpleVariantSubInspector.java
	MedSavantPlugins/medsavant.mendel-clinic/nbproject/private/private.xml
	MedSavantServerEngine/src/main/java/org/ut/biolab/medsavant/server/db/variants/VariantManager.java
	MedSavantServerEngine/src/main/java/org/ut/biolab/medsavant/server/ontology/OntologyManager.java
	MedSavantServerEngine/src/main/java/org/ut/biolab/medsavant/server/vcf/VCFParser.java
- Variant format standardized to annovar .avinput format, revamped VCF import.
- Added support for indels, insertions, and deletions
- Improved error reporting and logging.
- Revamped annotation system, much faster annotation speed.
- VCF files don't need to be sorted, although somewhat sorted VCFs will load faster.  (Sorting optimized for semi-sorted files)
- Added support for command line parameter 'medsavant.version'.  Running with -Dmedsavant.version=XXX will force server to run as version XXX.
- Fixes issues #239, #124.
- Issue #231 no longer applicable.
(cherry picked from commit 62916c36183f7b7c4f71f8a60975bada06dec0e3)
Added 'getFilteredVariantsForPatient' demo javascript method to testing.html of JSON project.
Fixed bug in previous commit.