Class AdapterUtility


  • public class AdapterUtility
    extends Object
    A utility class for matching reads to adapters. Note that this is different from ClippingUtility in that it tries to match the starts of reads to any part of the adapter (as opposed to finding the start of the adapter anywhere in the read).
    • Field Detail

      • DEFAULT_ADAPTER_SEQUENCE

        public static List<String> DEFAULT_ADAPTER_SEQUENCE
    • Constructor Detail

      • AdapterUtility

        public AdapterUtility​(List<String> adapterSequence)
    • Method Detail

      • isAdapterSequence

        public boolean isAdapterSequence​(byte[] read)
        Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
        Parameters:
        read - the basecalls for the read in the order and orientation the machine read them
        Returns:
        true if the read matches an adapter and false otherwise