amptk v1.2.0

• for all Illumina pre-processing methods the order of steps has been changed to now 1) search for primers/trim and then 2) merged PE reads. This ensures that all primer/adapter sequences are trimmed from dataset, whereas previously AMPtk releases merged PE reads first - because of how usearch/vsearch merge PE reads, occasional primer/adapter sequences were slipping through the pre-processing steps. Also reads with multiple primer hits (i.e. two forward primers) are now discarded. While this results in the pre-processing steps being slightly slower in runtime, it increases the data quality downstream.
• read orientation is tested/fixed on the fly for amptk illumina2 workflow (barcodes/primers in reads). Some datasets of 50/50 read orientation.
• added a check for "inverted OTUs" for all denoising/clustering steps. This was largely a check to validate that changing illumina pre-processing steps were working correctly (as unintended result was a small number of OTUs that were on the "crick" strand)
• Default mapping file now has a 'RevBarcodeSequence' column. Mapping files used for amptk illumina2 enforce the paired barcode sequences in the mapping file. If barcode fasta files are given, then all combinations of barcodes (5' and 3') are saved.
• a few py27/36 bug fixes