Revert "don't attempt to annotate SVs larger than 50 kb, since it causes memory issues. especially because GEMINI doesn't import them for variants > 50 kb"

This reverts commit 962f47105f192bf373b2e61ceaf383dc98404217.

undoing the commit allowing user to realign and write full BAM to null.
Judged this feature to have little use, and it obfuscates the code significantly