add outer flank regions for IlluminaBarcodeParser
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…in barcode parsing
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Added ability to parse second upstream / downstream region in
IlluminaBarcodeParserby addingupstream2anddownstream2parameters. Also modifiedIlluminaBarcodeParserso that reads will only be parsed if they are long enough to fully cover the region containing the barcodes and specified upstream / downstream sequences. Based on docs, this is how it was supposed to function before but did not. Additionally, this adds another row ("reads too short") to the fates from the barcode parser, as well as theouter_flank_fatesoption to report just failing the additional upstream and downstream regions.Related to allowing the
IlluminaBarcodeParserto be used to address this issue: jbloomlab/seqneut-pipeline#40