Report error if BAM index is not present

[bioinfo...@gringene.org]

When running TRUST for the first time, I came up against the following error:

UnboundLocalError: local variable 'ffu' referenced before assignment

In my usual way, I had a hunt through the code to see if there was anything obvious that could be fixed, but I found nothing. As a workaround, I put an explicit "ffu=None" at the start of the function. This allowed the code to run, but then I got an empty result from running TRUST:

----- Run TCR analysis -----
SRR1200516_vs_hg38_Aligned.sortedByCoord.out.bam
Screen for informative reads
['chr7', '142299011', '142813287', 'TRB']
[**no further output**]

After an hour or so of confusion, I remembered something about indexing in the instructions: "Please make sure that each BAM is paired with its index file". I fixed that, and got TRUST to run.

So... Could you please add something to the code to explicitly check for missing index files when those index files are needed?

[Bo Li]

Can you paste your commandline for running TRUST?

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