Package org.biojava.nbio.sequencing.io.fastq

Class Fastq

java.lang.Object
org.biojava.nbio.sequencing.io.fastq.Fastq
public final class Fastq extends Object
FASTQ formatted sequence.
Since:
3.0.3

  • Method Details

    • getDescription

      public String getDescription()
      Return the description of this FASTQ formatted sequence. The description will not be null.
      Returns:
      the description of this FASTQ formatted sequence

    • getSequence

      public String getSequence()
      Return the sequence for this FASTQ formatted sequence. The sequence will not be null.
      Returns:
      the sequence for this FASTQ formatted sequence

    • getQuality

      public String getQuality()
      Return the quality scores for this FASTQ formatted sequence. The quality scores will not be null.
      Returns:
      the quality scores for this FASTQ formatted sequence

    • getVariant

      public FastqVariant getVariant()
      Return the FASTQ sequence format variant for this FASTQ formatted sequence. The FASTQ sequence format variant will not be null.
      Returns:
      the FASTQ sequence format variant for this FASTQ formatted sequence

    • convertTo

      public Fastq convertTo(FastqVariant variant)
      Create and return a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant.
      Parameters:
      variant - FASTQ sequence format variant, must not be null
      Returns:
      a new FASTQ formatted sequence from this converted to the specified FASTQ sequence format variant
      Since:
      4.2

    • builder

      public static final FastqBuilder builder()
      Create and return a new FastqBuilder. The FastqBuilder will not be null.
      Returns:
      a new FastqBuilder