Open seyfim opened 4 years ago
Hey @seyfim thanks for reporting this. I'll have to take a closer look and see what's causing your issue, but I do see that the change from #28 is still present in plots.py: https://github.com/mdshw5/fastqp/blob/master/fastqp/plots.py#L528-L529. Your error is coming from the "mismatch plot" code path (https://github.com/mdshw5/fastqp/blob/master/fastqp/plots.py#L648) which should only be called when SAM/BAM files are provided. I can see that I implemented a check for SAM input files (https://github.com/mdshw5/fastqp/blob/master/fastqp/cli.py#L216), and count mismatches when the SAM format records are mapped, but it looks like when I call the mismatch plot code I don't have a check to make sure we encountered some mapped reads. Are you by any chance passing unaligned SAM/BAM files to fastqp? If so that would be something I didn't properly account for.
Hello @mdshw5 @ucpete @danielecook @tomsherborne @edawine , I am using python.2.7.12 and the following OS
I am getting the error
I checked the issues board, specifically the closed #26
which had a "hack-ish" solution #28 . In the source code (current version) the plots.py does not contain the lines mentioned
. Please advise!