Genome Alignment: Ref doesn't show gaps in translocations

[josiahseaman]

Followup #33.
When a chain representing a translocation is processed, the series of AlignedSpans are inserted into the existing composite alignment. These new alignedSpans do not appear to have query_tail_size > 0.
ChainParser.py ~ line 219

Observations

• Nematode alignment show no gaps anywhere
• In test_translocations with the full chr21, there are places with no ref gaps that still contain query gaps (image above)
• In test_whole_chromosome_alignment the master_chain shows gaps in both, other chains show gaps in neither.
• When that same chr7 N's chain is the largest chain in the file, there are query gaps, but no ref gaps.