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

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