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).
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean isAdapter​(htsjdk.samtools.SAMRecord record)
      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.
      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.
      boolean isAdapterSequence​(byte[] read, boolean revCompRead)
      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.
    • Field Detail

      • DEFAULT_ADAPTER_SEQUENCE

        public static List<String> DEFAULT_ADAPTER_SEQUENCE
    • Constructor Detail

      • AdapterUtility

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

      • isAdapter

        public boolean isAdapter​(htsjdk.samtools.SAMRecord record)
        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.

        Only unmapped reads and reads with MQ=0 are considers eligible for being adapter

      • isAdapterSequence

        public boolean isAdapterSequence​(byte[] read,
                                         boolean revCompRead)
        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
        revCompRead - When aligned reads are checked for being adapter, this specified if the original read had ben rev-comped during alignment.
        Returns:
        true if the read matches an adapter and false otherwise
      • 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