Class FastqFileIterator

java.lang.Object
org.snpeff.fileIterator.FastqFileIterator
All Implemented Interfaces:
Iterable<org.biojava.nbio.genome.io.fastq.Fastq>, Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
public class FastqFileIterator extends Object implements Iterable<org.biojava.nbio.genome.io.fastq.Fastq>, Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
Opens a fastq file and iterates over all fastq sequences in the file Unlike BioJava's version, this one does NOT load all sequences in memory. Thus it allows to process much larger files
Author:
pcingola

  • Field Details

    • debug

      public static boolean debug

  • Constructor Details

    • FastqFileIterator

      public FastqFileIterator(InputStream inStream, org.biojava.nbio.genome.io.fastq.FastqVariant variant)

    • FastqFileIterator

      public FastqFileIterator(String fastqFileName)

    • FastqFileIterator

      public FastqFileIterator(String fastqFileName, org.biojava.nbio.genome.io.fastq.FastqVariant variant)

  • Method Details

    • close

      public void close()
      Close file

    • getLineNum

      public int getLineNum()

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<org.biojava.nbio.genome.io.fastq.Fastq>

    • iterator

      public Iterator<org.biojava.nbio.genome.io.fastq.Fastq> iterator()
      Specified by:
      iterator in interface Iterable<org.biojava.nbio.genome.io.fastq.Fastq>

    • next

      public org.biojava.nbio.genome.io.fastq.Fastq next()
      Specified by:
      next in interface Iterator<org.biojava.nbio.genome.io.fastq.Fastq>

    • remove

      public void remove()
      Specified by:
      remove in interface Iterator<org.biojava.nbio.genome.io.fastq.Fastq>