Change using List instead of Array.
Use a list to store all feature location instead of dividing them into tx, cds and exon.
Change Location.java from an interface to a normal class. We didn't need this interface.
Update data sets structure. Add a data parser's reference to make a query more efficient...
Update data zoom selector.
Delete files what we really need not...
A sequence read contains more information than Alignment.
Update data writer and add more information.
Update features' structure.
Update annotation information.
Fix a severe bug when presenting the bam file.
Optimize the codes.
Use SAMFileReader.query to get reads by position instead of loading all reads into physical memory.
Modified by Data Writer.
Add a method to format chromosome name and get its alias name.
Update jar package...