Performance optimization: Reduced size of batch and the frequency of the output
Added annotation to ignore method Genotype.getAllelesIdx
Updated version of datastore-mongodb due to bugfix
Better support for missing genotypes
Empty reference and alternate alleles accepted as arguments for filtering variants
biodata ArchivedVariantFile class renamed to VariantSourceEntry
AlignmentStorageManager and MongoDBAlignmentStorageManager fixed
VariantStorageManager and MongoDBVariantStorageManager fixed
OpenCGAStorageMain and FileWSServer fixed
Minnor changes and bug fixes
StorageManager methods return an URI for generated files.
Added storage microservice skeleton
Added command "search-variants" in OpenCGAStorageMain
Added command "search-alignments" in OpenCGAStorageMain
Added FilesServlet.java to storage microservice
storage-app: Accepts GFF for multi-region searchs.
Merge remote-tracking branch 'opencga/develop' into feature/refactoring

Conflicts:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/OpenCGAMain.java
	opencga-server/src/main/java/org/opencb/opencga/serverold/VariantWSServer.java
	opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/io/json/ArchivedVariantFileJsonMixin.java
	opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/DBObjectToArchivedVariantFileConverter.java
	opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/DBObjectToSamplesConverter.java
	opencga-storage/opencga-storage-mongodb/src/main/java/org/opencb/opencga/storage/mongodb/variant/VariantMongoDBAdaptor.java
	opencga-storage/opencga-storage-mongodb/src/test/java/org/opencb/opencga/storage/mongodb/variant/DBObjectToArchivedVariantFileConverterTest.java
	opencga-storage/src/main/java/org/opencb/opencga/storage/variant/json/ArchivedVariantFileJsonMixin.java
	opencga-storage/src/main/java/org/opencb/opencga/storage/variant/json/VariantSourceEntryJsonMixin.java
	opencga-storage/src/main/java/org/opencb/opencga/storage/variant/mongodb/DBObjectToArchivedVariantFileConverter.java
	opencga-storage/src/main/java/org/opencb/opencga/storage/variant/mongodb/DBObjectToVariantSourceEntryConverter.java
	opencga-storage/src/test/java/org/opencb/opencga/storage/variant/mongodb/DBObjectToArchivedVariantFileConverterTest.java
	opencga-storage/src/test/java/org/opencb/opencga/storage/variant/mongodb/DBObjectToVariantSourceEntryConverterTest.java
	pom.xml
catalog: Updated version of datastore-mongodb for CatalogMongoDBAdaptor
daemon: Handled "override output files" and "execution error" on Jobs and Indexes.
storage: datastore dependency updated to 0.3.0