One thread not use multithreaded

[martinghunt]

• when threads == 1, do not use the mlutithreading module. This helps debugging as mluitthreading is stopping getting a proper stack trace.
• Keep flushing log files, so if ariba crashes, at least the log files are up to date.
• When there is >1 indel in a single codon, the code can't yet handle it. This forces a line in the report with 'INDELS' in the variant effect column, so at least we know when it's happening. Should be rare, but utlimately needs handling properly.