Portcullis junc detects no junctions if bam index file already present in bam dir #60
Description
Not sure if anyone can reproduce but I am having an issue where Portcullis fails to find any junctions in a bam file when a pre-existing index (.bai) file is present in the same directory as the input bam file. Reindexing before running portcullis does not seem to solve, only deleting or moving the existing index file from the same directory as the input bam file.
It also seem to be producing warnings 'Warning: The index file is older than the data file: ' even though this is not the case. Is it using the date stamp on the newly created symlink to the bam for the date comparison?