RNA: add rna-specific controls to sv candgen

Add a new rna flag to filter likely introns from the
sv candidates and increase the reference context for
the jump aligner.

Patches reordered from original rna branch for master
MANTA-119 create shared aligner backtrace logic
RNA: add intron jump aligner

Adds shared base class to store common backtrace logic
between jump and intron-jump aligners + new unit tests
RNA: switch to intron jump aligner in rna mode
refresh code styler