Fixed bug in Alignment.equals
Merge branch 'develop' of https://github.com/jmmut/java-common-libs into develop
Merge branch 'develop' of https://github.com/j-coll/java-common-libs into develop
Fixed stuff.
Removed debug lines
Merge branch 'develop' of https://github.com/jmmut/java-common-libs into develop

Conflicts:
	bioformats/src/main/java/org/opencb/commons/bioformats/alignment/tasks/AlignmentRegionSummarizeTask.java
Fixed AlignmentHelperTest getSequenceFromDifferences and getCigarFromDifferences
Added shortReferenceSequenceException for AlignmentHelper Methods.