Bug: link features.tsv points to wrong file for SJ

[ms-gx]

I am referring to the output if running --soloFeatures SJ.

The link which is generated in SJ/raw does point to a generic ../../../SJ.out.tab instead of the real filename.

[alexdobin]

This link is supposed to point to SJ.out.tab file in the main directory - these are the "features" for the SJ option.

[ms-gx]

What I mean is that the path is wrong. It is not pointing to the SJ.out.tab in the main directory.

[alexdobin]

Are you using --soloOutFileNames option? This can screw up the sym-link.

[ms-gx]

No, I am not using --soloOutFileNames.

But the symlink for SJ/raw/features.tsv points to ../../../SJ.out.tab. Whereas the actual path is ../../../MAPPING_A3_48h_SJ.out.tab.

[alexdobin]

I see the problem now, this happens if a prefix is specified for the output files. I will work on fixing it.

[ms-gx]

Thanks Alex!