Remove prefix chr-chrm from chromosome
Removed prefix chr/chrm from cchromosome. If position is negative then the system throws an Exception
All combinations of chrom prefix replaced in Variant, some methods made final
First modifications for Alignment->SAM conversion
Start and end from AlignmentRegion takes into account unclipped start and end.
Bug fix on getDifferenceFromCigar when refSeq is null
Added first aproximation for getSequenceFromDifferences
Merge branch 'toSAM' of github.com:j-coll/java-common-libs into toSAM
Added AlignmentRegionCompactorTask
CompleteDifferencesFromReference in AlignmentHelper
Refactor: Moved AignmentTasks to package tasks.
Merge branch 'develop' of github.com:opencb/java-common-libs into develop