Fix #8731
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Fix #8731
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I have made it that alleles that get pulled in through the --alleles argument must overlap the calling interval for the assembly region in question. This was causing problems where extremely long deletions that that are longer than the assembly window padding could get pulled in in the alleles list and cause exceptions in the code that does not expect events to span past the begining of the assembly window.
This should not change results in any signficant way since we already filter out any events that are outside of the calling window before genotyping the event. This prevents us from even genotyping and HMM scoring events that start before the spanning window. This is a hack solution to the problem posed in #6339.
Fixes #8675