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Genome Alignment: Ref doesn't show gaps in translocations #74
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.
Followup #33. When a chain representing a translocation is processed, the series of
AlignedSpansare inserted into the existing composite alignment. These new alignedSpans do not appear to havequery_tail_size> 0. ChainParser.py ~ line 219Observations
test_translocationswith the full chr21, there are places with no ref gaps that still contain query gaps (image above)test_whole_chromosome_alignmentthe master_chain shows gaps in both, other chains show gaps in neither.