New AlignmentStorageManager and MongoAlignmentStorageManager implementation. Includes:

-Generic StorageManager
-MetaData class to manage indexed files
-New IndexedAlignmentDBAdaptor to query regions.
-Tests

TODO: Calculate coverage in MongoAlignmentStorageManager. Storage in Mongo.
Added new SqliteSequenceDBAdaptor for Fasta storing. Extends SequenceDBAdaptor
Merge branch 'feature/MongoAlignments' into feature/refactoring_merging
Fixed 1-based region query on SqliteSequenceDBAdaptor
Imported AlignmentJson reader and writers from old schema.
Imported AlignmentCoverageCalculatorTask and made code cleaning.
Imported AlignmentRegionCompactorTask. Now uses SequenceDBAdaptor.
Added ComplexTypeConverters for coverage objects.
Added CoverageMongoWriter and query "getCoverageByRegion". Changed StorageManager interface.
Sorting MeanCoverage before write in json.
Added IndexedAlignmentDBAdaptorTest.testGetCoverageByRegion
Merge branch 'feature/refactoring' into feature/MongoAlignments
Changed properties management in AlignmentStorageManager
Merge branch 'feature/refactoring' into feature/MongoAlignments

Conflicts:
	opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/StorageManager.java
	opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/alignment/AlignmentStorageManager.java
Completed MongoDBAlignmentStorageManager.transform
Imrpoved IndexedAlignmentDBAdaptorTest
Now getCoverageByRegion calculates from bam instead of query mongo.
RegionCoverage is not saved in mongo.
IndexedAlignmentDBAdaptor.getAllAlignmentsByRegion return AlignmentRegion instead of List<Alignment>

With INCLUDE_COVERAGE=true, calculates the coverage for this region.
Added fields "chr", "start", "size" to each document.
Added mongo aggregation for histogram values
Merge branch 'feature/refactoring' into feature/MongoAlignments

Conflicts:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/OptionsParser.java