error in breaks

[avilella]

Hi,

I spotted an error with some of my samples, see below. This could be due to not having enough reads, but I was wondering if there is a better way of knowing if that's the case:

2017-12-14 11:44:03 ichorcna STDERR Slurping: .//CEG60-120-8PC_S16_L00.bml.GRCh38.karyo.deduplicated.icna.wig
2017-12-14 11:44:03 ichorcna STDERR Error in (breaks[i] + 1):(breaks[i + 1] - 1) : NA/NaN argument
2017-12-14 11:44:03 ichorcna STDERR Calls: wigToRangedData
2017-12-14 11:44:03 ichorcna STDERR Execution halted

[gavinha]

Hi Albert,

This is a good point. The wigToRangedData function is a HMMcopy R/Bioconductor function. We can try to better catch this error and output an appropriate error message.

Thanks for bringing this up. Best, Gavin

[applebyn]

Hello Gavin, Did you come up with a solution for this error? I'm getting the same message with my .wig file.

BW, Niamh

[EvoMedLab]

For me it was an empty mappability line in the wig generated by HMMcopy