Restrict assembly contig anchor to SV anchoring reads

[d-cameron]

• Don't assemble any reads not providing support for the breakend contig being assembled
• Pad contig anchor with Ns when there are gaps in reference support

[d-cameron]

SC/ASC annotations cannot be used for variant linking/phasing if local assembly are included as the assembly anchor is not restricted to reads that support the SV. In the HMF cohort (4000 WGS samples, ~90x coverage), around 2/3 of assembly contigs extended past their linked SV (which is bad).

The work-around for this is to remove local assemblies from these annotations until this issue is
resolved at the assembly stage.