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cnobles / dualDemultiplexR

[Depreciated, see nuckit repo] Demultiplex Illumina FASTQ files using dual barcodes (I1 and I2).
GNU General Public License v3.0
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Ambiguous nucleotide matching with Biostrings::vmatchPattern() #3

Open cnobles opened 7 years ago

cnobles commented 7 years ago

May be able to knock out the ambiguous code matching with Biostrings::vmatchPattern(), using the fixed = FALSE or "subject" options (TRUE is default which won't allow for ambiguous matching).

There should be a performance increase with the switch from pairwiseAlignment() to vmatchPattern(), but may not be much.

Biostrings::vmatchPattern() is better suited for the task than pairwiseAlignment, though both can be used.