rtgtools: Add truth set filtered by bait set for WES samples

[peterpru]

Description of the bug

When doing rtg vcfeval on exomes, we need to filter the truth sets based on the coordinates of the bait sets, otherwise it will inflate the number of missed SNVs outside the boundaries of the baits.

Proposed solution, when analysis_type = WES, switch to alternative input file for the truth set.

Command used and terminal output

No response

Relevant files

No response

System information

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