Class FastqTrimmer

  • Direct Known Subclasses:
    FastqTrimmerMedian

    public class FastqTrimmer
    extends java.lang.Object
    Trim fastq sequence when quality drops below a threshold The resulting sequence has to ba at least 'minBases'
    Author:
    pcingola
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  
    • Constructor Summary

      Constructors 
      Constructor Description
      FastqTrimmer​(int qualityThreshold, int minBases)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      org.biojava.nbio.sequencing.io.fastq.Fastq trim​(org.biojava.nbio.sequencing.io.fastq.Fastq fastq)
      Create a new fastq sequence by trimming the given sequence
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • debug

        public static boolean debug
    • Constructor Detail

      • FastqTrimmer

        public FastqTrimmer​(int qualityThreshold,
                            int minBases)
    • Method Detail

      • trim

        public org.biojava.nbio.sequencing.io.fastq.Fastq trim​(org.biojava.nbio.sequencing.io.fastq.Fastq fastq)
        Create a new fastq sequence by trimming the given sequence
        Parameters:
        fastq -
        Returns: