Ref sequence output for sequencer.py is a concatenation of the mut and wt #234
Description
Describe the bug
Line 104 is a concatenation of wt + mut ref seqs. This eventually gets output to the molecules file as part of the returned alignment on line 135. The alignment is performed correctly. It is just the output reference sequence that is like this.
To Reproduce
Run an analysis with a vcf containing mut seqs. Look at the column ref_seq in molecules.tsv file generated.
Expected behavior
The best scoring alignment reference sequence would be output.
Screenshots
