Added method to AbstractAnnotation to get set of blocks
Added getBlockSet() method to Annotation interface
(1) Removed numBlocks variable because it was not being updated
correctly, and changed references to call size() on the set of blocks.
(2) Fixed a bug that was causing extra blocks to be added: when adding a
new block that overlaps an existing block, we were adding a merged block
and keeping the old overlapper. The fix was to remove the original
overlapper in this case. (3) Fixed a minor off-by-1 error in
getRelativePositionFrom5PrimeOfFeature().
Added methods to get UTRs
When getting the blocks of a PairedMappedFragment, don't just get each
read separately because they might overlap. First make a
BlockedAnnotation with the two reads, which takes care of overlapping
blocks, then get the blocks of the BlockedAnnotation.
Added minor output messages when writing paired end bam file.
Crash if there is no active DRMAA session
Test for number of reads in populated windows.
Added some functionality to StringParser.