Changed EBI DbFetch code so that the function works again. Added latest picard jar. More work on CRAM file loading. Updated/added scripts for application start. Small tweaks to makefile/ant. Removed gff2embl and gene_builder. Recreated evosuite tests.

Initial BAM View changes to fix selection issues, zooming into secondary alignments, erroneous collapsing of reads with same start/end position and display of SNPs - related to RT ticket 597652

First commit of unit test changes. Added more manual unit tests, an EvoSuite regression set and coverage reporting. Moved Java version for Artemis to Java 8. Ripped out redundant Corba code.

Building from source without this patch resulted in the following error:
artemis-16.0.0+dfsg/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java:35:
error: CRAMReferenceSequenceFile is not abstract and does not override abstract method close() in ReferenceSequenceFile

user_default_min_window in the options file