I am fairly certain that this exact issue is still open, and so have
opened a bitbucket ticket to track progress:
If this has been corrected already, one of us will send an update tomorrow.
On 9/3/11 4:41 PM, Florian Wagner wrote:
when a tool outputs an unsorted bam file, the indexing fails (quietly)
and its metadata variable "bam_index" points to an inexistent file. This
causes a nasty bug when trying to import the dataset into a data library
and actually makes the library unusable unless you delete the broken
entry from the - in my case Postgresql - database by hand. Are you
working on it?
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