enable plate-level indices as upstream2 in barcode parsing

[jbloom]

Configured to enable plate-level indices to be embedded in the round-1 PCR primers (see this issue). Essentially, this amounts to allowing a per-plate flanking sequence to be specified for each plate, and only FASTQ reads with that flanking sequence are read for that plate. Typically this index would be specified as upstream2 in the illuminabarcodeparser. To enable this change, altered the configuration from the previous setup of just having a single global illumina_barcode_parser_params applied to all plates. Now such a global parser is still specified that has default values that you want to apply to all plates. But in addition, in the per-plate configuration you can specify illumina_barcode_parser_params that are added to (and override) anything in the global parser params, and can contain plate specific upstream2 and other relevant setting (eg, upstream2_mismatch). The test example was modified to use this option for plate2 and plate11.