Improved AlignmentSamDataWriter and getSequenceFromDifferencesTest.

AlignmentSamDataWriter is not tested yet.
Other minor changes.
Merge branch 'develop' of https://github.com/j-coll/java-common-libs into develop

Conflicts:
	bioformats/src/test/java/org/opencb/commons/bioformats/alignment/AlignmentHelperTest.java
Changed Alignment attributes to Map<String, Object>

It is needed to keep the type (of the Map value) to write the tag properly in
AlignmentDataWriters.
Fixed imports