Hello Galaxy Team,

I get this error

> "Error reading bam file. This usually indicates a problem with the index
> (bai) file. ArrayIndexOutofBoundsException: 6921 (6921)."

 when I finish my pipeline and try do view any of the sam or bam files.
-occurs on both hg19 and hg_g1k_v37
-i tried to sort and index the sam file from step 22 and 25 in igv, but
without success and ideally I do not want to have any steps outside Galaxy.
-I get the error on the data of step 44, 38 and 35

Opening the sam file from step 25 gives: "could not find index" and after I
use the tools in IGV it works and I can look at the aligned sequences, but
still this is a step outside of Galaxy, which I do not want.

Anything I overlooked? I'd appreciate every hint.

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