Package org.snpeff.fileIterator
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
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionFastqFileIterator
(InputStream inStream, org.biojava.nbio.genome.io.fastq.FastqVariant variant) FastqFileIterator
(String fastqFileName) FastqFileIterator
(String fastqFileName, org.biojava.nbio.genome.io.fastq.FastqVariant variant) -
Method Summary
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Details
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debug
public static boolean debug
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Constructor Details
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FastqFileIterator
public FastqFileIterator(InputStream inStream, org.biojava.nbio.genome.io.fastq.FastqVariant variant) -
FastqFileIterator
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FastqFileIterator
public FastqFileIterator(String fastqFileName, org.biojava.nbio.genome.io.fastq.FastqVariant variant)
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Method Details
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close
public void close()Close file -
getLineNum
public int getLineNum() -
hasNext
public boolean hasNext() -
iterator
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next
public org.biojava.nbio.genome.io.fastq.Fastq next() -
remove
public void remove()
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