Hi, I'm trying to run IntEREst on BAM files from a single-ended experiment. It runs for a while, then I get an error:

Error in interestAnalyse(reference = reference, bamFile = bamFile, isPaired = isPaired,  :
  object 'resTmpPair' not found
Calls: do.call ... mapply -> <Anonymous> -> interest -> interestAnalyse

I checked the source for the current version and the development version of the package, and it looks like resTmpPair is assigned in an if-block and then later there's an attempt to reference it outside that scope.

The following relevant (abbreviated) lines are in both interestAnalyse.R and interestAnalyse.sequential.R.

if(isPaired){ (line 52 in current version)
....
resTmpPair<- BiocParallel::bpiterate... (line 63 in current version)
}
if(isPaired & (length(resTmpPair)>0)){... (line 121 in current version)

As such, it seems that running any single-ended dataset would result in resTmpPair being referenced before being defined.

Hi dear Adam!

I found the possible cause of the error and added a couple of lines that should fix the error.

Thank you for reporting the error and feel free to let me know if you had other problems.

The updates are available in the IntEREst-devel on GitHUb (https://github.com/gacatag/IntEREst) immediately and on Biocondcutor (devel) page with a bit of delay. After performing test runs I'll also implement the changes to the release version of IntEREst.

Cheers,

Ali