Which flagstat output categories are passed by Tophat to Cufflinks for analysis?

Question

[trakhtenberg]

flagstat (samtools) output "with itself and mate mapped" includes "properly paired" output but not "singletons" output. What from within these is passed by Tophat to Cufflinks for analysis? "Properly paired" are passed, "singletons" appears from here are excluded, but what about the extra pairs in the "with itself and mate mapped"? Is there a reason to think that splice junctions reads may be enriched in these extra pairs?