Whitespace
Use builds directly instead of passing model-ids and refinding them.

This otherwise might lead to using a different build than is set as
the input to the ClinSeq build and mixing builds used within a single
run.
Remove newlines from error messages.
Simplify die($self->error_message) calls.
Simplify BAM data structure.
Extract subroutine to grab data for a SomVar build.
Extract subroutine to grab data for an RnaSeq build.
Replace with a newer (actually succeeded) build.

This is still bad... but it passes again (for now).
Remove commented-out code.
Remove comment banners.
Whitespace.
Add true value.
Use accessor to find transcript_info file.
Move up reference check; remove disused display name.
Remove unused variables.
Centralize fasta lookup.
Access annotation build directly from input build.
Move up check for succeeded builds.
Merge pull request #91 from tmooney/use_input_builds

Use Input Builds instead of Models in ClinSeq GetBamReadcounts