add check for transcript length before querying UTR sequence

[shenkers]

I have been running into an issue with Funcotator where some mutations are causing Funcotator to crash because it attempts to query a segment that extends beyond the boundary of the transcript ( see #6345 )

This pull request addresses the issue by adding a check for transcript length before executing the query. I looked at the code, and Funcotator currently handles problematic sequence queries in getFivePrimeUtrSequenceFromTranscriptFasta() by returning an empty string. I modified getFivePrimeUtrSequenceFromTranscriptFasta() to also return an empty string when the segment it is trying to retrieve extends beyond the boundary of the transcript.

I have a small VCF that can be used to reproduce the problem using the current code on master and the hg38 data source, and I have verified that this pull request allows Funcotator to process the problematic variant without crashing. I did not add the VCF to the tree, but can provide it if that is preferred. Is there any guidance for how to implement integration tests with funcotator? The Funcotator data source I am using is ~12gb, but I would think the problem could be reproduced with 1 transcript and 1 variant.

This is my first pull request to GATK, so please let me know if there is anything you would like me to adjust, I'm happy to address any comments.

[jonn-smith]

Hi @shenkers - thanks for the PR. I'll take a look.