Comment added to Basic annotation
Using white space instead of tab to make gene from bed in Gene.
Major change made to AlignmentModel.Cache

When updating the cache, if the number of reads being added to the
interval tree is more than 500,000 the free memory available is checked.
If the memory used is more than 80% and thus, the free memory is less
than 20% of the total memory available, the cache is aborted and we
return the iterator over the entire region without using the cache. The
problem regions are stored in the cache class object so that if the
program tries to get reads over this region again, it will know that it
must not use
* Bugs fixed in AddEndRNASeqToScripture.
* ConnectDisconnectedTranscripts is added to connect disconnected
reconstructions using the insert size of the library along and checking
for spanning paired end reads.
* Small changes to Scripture
Classify Reconstructions is a downstream class to Scripture to remove
all reconstructions mapping to supplied annotation sets.
Debugging statements added to PairedEndWriter.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git
Java Documentation added