autobin command -o parameter

[andyjslee]

It would be great if the 'autobin' command allowed -o (output) parameter to determine where to write the target.bed and antitarget.bed files. Thanks!

[etal]

I agree, thanks for the suggestion.

[etal]

autobin now lets you set output paths directly: --target-output-bed FILENAME and --antitarget-output-bed FILENAME (v0.9.14). That covers directing the generated target/antitarget BEDs to specific paths, which was the request here, so closing. (There's no single -o/--output-dir umbrella flag; if a directory-style option mirroring batch --output-dir would help here, a feature request is welcome.)