indexcov: producing .html but no other files about goleft

[brentp]

before we debug further, can you try with:

goleft indexcov -d test-dir *.bam --sex ''

and then see if test-dir/index.html works?

[brentp]

can you use either: https://github.com/brentp/goleft/releases/download/v0.1.10/anonymize-for-indexcov_linux64
or https://github.com/brentp/goleft/releases/download/v0.1.10/anonymize-for-indexcov_osx depending on your OS and send me a zip of the result. It basically sends in the index and the bam header, which I use for knowing what the chroms, lengths are. and it removes any sample info.

[stephenwilliams22]

Hi Brent,
Thanks for the response. I think I have been misinterpreting this command all along. My thought was that the -d option was for the directory of the .bam files not the output directory. It worked now and I'm pretty sure I'm good to go. Sorry for the confusion!

[brentp]

ok. well that's good. When you opened the issue, I tested with -d . and it worked fine for me so I thought it might be something else.
I'll close for now, but please let me know if you hit other issues.