Added Alignment Data Reader and Writer
Added CoverageCalculator and AlignmentCoverageRunner
Merge branch 'develop' of github.com:opencb/java-common-libs into develop
Initial code for AlignmentTabixDW
Improved AlignmentCoverageRunner. Now extends AlignmentRunner.
Merge branch 'develop' of github.com:opencb/java-common-libs into develop
Moved IncrementalList to commons
Merge branch 'developColl' of https://github.com/aaleman/java-common-libs into develop
Merged developColl.

Added test file path comprobation.
Merge branch 'develop' of github.com:opencb/java-common-libs into develop
Added Alignment files for Coverage Task

AlignmentCoverageCaltulatorTask
AlignmentDataReader (Sam/Bam)
Merge branch 'feature/newRunners' of github.com:opencb/java-common-libs into feature/newRunners
Reordered files
AlignmentCoverage now uses the CIGAR.

In addition to the regular coverage, it takes into account the offset of a
deletion or insertion.
Added length in AlignmentDifference.

When the difference is too large, it is not stored completely.
Now AlignmentDifference might not store reference sequence.

To use AlignmentDifference.seq now, you will have to ask if in this
AlignmentDiference isSequenceStored().

This was done to improve performance in those algorithms where you need CIGAR
information, but not the reference sequence of the read. This way we avoid
asking it to cellbase in every alignment.
Now AlignementHelper can handle a null reference sequence.

If getDifferencesFromCigar recieves a null as refStr, it means that it is not
needed to store the reference sequence in the AlignmentDifference(s).

Updated AlignmentSamDataReader.
Merge remote-tracking branch 'opecb/feature/newRunners' into feature/newRunners
Minor changes:
Files moved to new location.
Some Files removed.
Merge branch 'develop' of github.com:opencb/java-common-libs into develop