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nghiavtr / FuSeq

GNU General Public License v3.0
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broken code #13

Open linuxbioinfoguy opened 4 years ago

linuxbioinfoguy commented 4 years ago

Hi, when executing, it broken and show the message as follow:

Checking possible paralogs... Post processing mapped reads (MR)...Error in 1:nrow(junctBr$myFusionFinal) : argument of length 0 Calls: postProcessMappedRead -> refineJunctionBreak Execution halted

But I could not find any line with the pattern "1:nrow(junctBr$myFusionFinal)" in the R code.

Thanks

J

nghiavtr commented 4 years ago

Hi,

Sorry for this bug. The error should be from function refineJunctionBreak() called from postProcessMappedRead (). The R code of this function can be found in FuSeq_functions.R I am not sure what happened but it is likely that in your data there are no fusion candidates discovered from the mapped-read pipeline.

Best, Nghia

linuxbioinfoguy commented 4 years ago

Thanks, let's see if I could fix that, the reason is that even there is no fusion detected, it probably better to keep the script unbroken and generate a report even it is empty.

Thanks

J

nghiavtr commented 4 years ago

Right, it should run smoothly. I will try to fix this in the next version of FuSeq. Thank you for reporting this bug.

Best, Nghia