How does COBRA handle joining two query sequences?

[LSHillary]

Hi Linxing,

Great tool. I'm really interested in using it with some of my datasets. One question that came up in discussing COBRA with others was how it handles cases where e.g. Query Contigs Q1 and Q2 could be joined by non-query contigs, e.g. Q1-c1-c2-Q2. Apologies if I missed this part of the manuscript but does COBRA have the ability to handle this, or does it start from the assumption that it is only looking for ways it can extend query contigs in isolation?

Best,

Luke