GemMappabilityToBed has problems with some invalid characters in mappability files

[robmaz]

GemMappabilityToBed produces user errors with files generated by gem-mappability. I am attaching the files in question and the output of gem-mappability and readtools.

map2bed.out.gz
mappability_files.tar.gz
mappability.out.gz

[magicDGS]

@robmaz - thanks a lot for using an experimental tool and reporting an error, it is much appreaciated!

First, I should recognized that I found this before in one of my analyses, and when I dig into the problem was a corrupted run of the gem mappability command. Thus, I am afraid that the problem is not in ReadTools but there. That's why I contacted the authors of gem3 to know when they'll include the tool in the new implementation.

Could you try to re-run the gem mappability command for one of your input FASTA, and let me know if it fails in the exact same chromosomal position? In that case, that means that it might be a ReadTools problem; otherwise, the gem command should be re-run until it does not procude a writing error (that's the reason of the null character).