IHOMLEN sometimes incorrect for small duplications

[d-cameron]

Since BreakpointHomology truncates flanking sequence to the length of the event, short tandem duplications sometimes incorrectly report homology.
hg19 example

4	63534532	gridss25_35352o	T	]4:63534640]T
4	63534640	gridss25_35352h	A	A[4:63534532[	

Reports an inexact homology of 109bp since the remote flanking sequence aligns to the duplication instead of the anchor.

Defensive programming: don't report IHOMLEN if less than X% of anchor sequence isn't mapped in the alignment

Fix:

• extend the anchoring sequence to always be longer than the alignment

• Retest small DEL, DUP, both INV orientations, and INS events with and without homology to ensure correct behaviour for all simple events

• Test DEL and DUP with untemplated inserted sequence