Get id from file basenames with dir input

[tlitfin-unsw]

This solves a bug with directory input in the case that multiple files have the same fasta header for the first entity (eg 2 multimers (AxB and AxC))

• This generates samplesheet id from file basename rather than fasta header.
• The fix loses the theoretical ability to split a directory of multy-entry fastas in to separate monomers but this potential edge-case functionality is not currently used with KOD.