Merge branch 'fix-gentrap_strandspec' into 'develop'

Fix strand-specific separation in Gentrap

This fixes a bug caused by incorrect creation of plus and minus strand BAM files.
It was caused by incorrectly specifying the SAM flags, causing the plus and minus
strand BAM files to still contain mixed strand reads.

The fix has been tested in SHARK and confirmed to work.

See merge request !230