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If -c is not used when calling RNABuilder, program goes ahead and uses contacts.dat. This can be confusing for users if they did not intentionally leave off the -c option.
Telling users that contacts.dat is the default would be good.
One possible solution is that the first output line reiterates the input file used:
"Using input file: XXXXXXX" . Could also serve as solution for bug #857 since presumably if none was found, that message would be telling ...
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