Class FastqTrimmer

java.lang.Object
org.snpeff.fastq.FastqTrimmer
Direct Known Subclasses:
FastqTrimmerMedian

public class FastqTrimmer extends 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
     
  • Constructor Summary

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

    Modifier and Type
    Method
    Description
    org.biojava.nbio.genome.io.fastq.Fastq
    trim(org.biojava.nbio.genome.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 Details

    • debug

      public static boolean debug
  • Constructor Details

    • FastqTrimmer

      public FastqTrimmer(int qualityThreshold, int minBases)
  • Method Details

    • trim

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