> Are we the only ones that are missing bam index files (the .bai) when 
> exporting a history that contains for instance bowtie mapped reads.

Bam indices are deliberately left out because they can be regenerated. However, 
it's reasonable that there should be an option to download BAIs; I've added it 
to the card for improving history import/export.

> In the original history we can save the bam and bai files but after export to 
> a file (tgz) and later import into another (or the same) galaxy instance, the 
> bai files cannot be accessed/saved anymore....

This is a bug and has been fixed in -central changeset 3a71d40d7b99

J.



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