Index not found with symlinked files

[fbdtemme]

I have a directory with a cram and cram index file which are both symlinks.

9876T.recal.crai -> /home/fbdtemme/Documents/sarek/work/stage/32/6f1c18/9876T.recal.cram.crai
9876T.recal.cram -> /home/fbdtemme/Documents/sarek/work/stage/2f/682545/9876T.recal.cram

When running msisensor-pro baseline in that directory with a configuration file containing this:

9876T   9876T.recal.cram

it complains that the crai index is not found.

If I copy to index file to /home/fbdtemme/Documents/sarek/work/stage/2f/682545/ it works. msisensor-pro seem to resolve the symlink to its realpath and looks into the directory there, instead of looking in the path of the symlink.

[PengJia6]

Thanks for your suggestion, we will fixed in next release!