refine_assembly fix for empty reads input

[dpark01]

assemble.refine_assembly had been resilient to receiving empty reads (and empty reference) input, but not when --already_realigned_bam was specified (which is how our WDLs currently use this).

This PR:

• adds a unit test for empty bam input to refine_assembly using --already_realigned_bam (initially failing)
• adds a code path to handle this scenario properly
• and now passes the new test