Hi - Thanks for the info.  I had two versions of samtools installed so I 
uninstalled one and left only samtools 0.1.19 however I still get the error.  
I'm using the tophat2 tool and I'm still getting the error.  I just reinstalled 
the tophat2 tool and I'm running it again.

> On Feb 23, 2015, at 8:23 AM, Saket Choudhary <sake...@gmail.com> wrote:
> On 22 February 2015 at 23:17, Michael Thon <mike.t...@gmail.com> wrote:
>> bam_index_build2() not yet
> Hi Michael,
> This seems to be related to this:
> https://github.com/samtools/samtools/issues/199
> You should probably switch to samtools 0.1.19
> Saket

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