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Sync with Cactus#55

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glennhickey wants to merge 2 commits into
gsneha26:mainfrom
ComparativeGenomicsToolkit:merge-up
Open

Sync with Cactus#55
glennhickey wants to merge 2 commits into
gsneha26:mainfrom
ComparativeGenomicsToolkit:merge-up

Write empty (rather than invalid) output when no alignment found

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