Hello,

I am using the function matchGenes of the package bumphunter to associate
many regions of interest with transcripts.

I use all=TRUE in order to get several results per region.
When I use all=TRUE and a small amount of queries, the output indeed
contains the columns 'queries' and 'Tx' which give the query index and the
matching transcript.
But when I use all=TRUE and many regions (when the function starts to split
the data), the output data.frame does not contain anymore these two columns
and it is not possible to know which region is associated with which
transcript.
I think there is a problem in the function when the annotation is split
into chunks of 10000 regions each.

Please let me know if it can be solved!

Best regards,
Anne

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