sga index output unexpectedly placed in working directory

[marcelm]

When running

sga index --no-reverse directory/file.fastq

I would have expected the index files that are created to be directory/file.bwt and directory/file.sai, but they are actually put into the working directory as file.bwt and file.sai. This can be worked-around by using the -p option, but is still unexpected behavior that makes sga index a little harder to use in automated workflows.

[jts]

This was an issue I considered but ultimately decided to strip the leading directories when generating on the output name. I'm not sure that I made the right decision. I agree its more intuitive to leave the directory intact. This would be a large change to the behaviour as the subsequent programs (correct, overlap, etc) look in the current working directory for the index. I'm going to think this over for a few days.

[mmokrejs]

No don't it is a good idea to force all output to cwd. I agree with @marcelm .