croak instead of die

It's a non-unique pattern which caused the failure so die from caller's
perspective (croak).
add option to filter results from glob on pattern

Maintains support for glob pattern but allows flexibility when needed.
get tier bed path from Tier result
only generate IGV XML files for known references
fix issues for RT/100194

- only generate IGV XML files for known references
- get tier bed path from Tier result