Different length reads for R1 and R2

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The sequencing library I am dealing with requires trimming of 15 bases on the 
reverse read only, so I end up with 100 base Fwd read and an 85 base Rev read. 
When I run chimerascan with these files it gives me an error that the pairs are 
different lengths. I decided maybe that was just a sanity check, so I commented 
out the check for equal length pairs and re-ran it. It seems to run ok. Is 
there any issue with this? Do reads have to be the same length?

I did notice that when looking for discordant reads there were some errors 
saying something like:
2014-10-16 16:15:12,503 - root - WARNING - Could not extract sequence of length 
>101 from 5' partner at gene_uc031ret.1:0-42, only retrieved sequence of length 
42
but I am not sure this is related?

Original issue reported on code.google.com by [email protected] on 20 Oct 2014 at 6:57