Package org.snpeff.fileIterator
Class FastqFileIterator
- java.lang.Object
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- org.snpeff.fileIterator.FastqFileIterator
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- All Implemented Interfaces:
java.lang.Iterable<org.biojava.nbio.genome.io.fastq.Fastq>
,java.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
public class FastqFileIterator extends java.lang.Object implements java.lang.Iterable<org.biojava.nbio.genome.io.fastq.Fastq>, java.util.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 Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description FastqFileIterator(java.io.InputStream inStream, org.biojava.nbio.genome.io.fastq.FastqVariant variant)
FastqFileIterator(java.lang.String fastqFileName)
FastqFileIterator(java.lang.String fastqFileName, org.biojava.nbio.genome.io.fastq.FastqVariant variant)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
close()
Close fileint
getLineNum()
boolean
hasNext()
java.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
iterator()
org.biojava.nbio.genome.io.fastq.Fastq
next()
void
remove()
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Constructor Detail
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FastqFileIterator
public FastqFileIterator(java.io.InputStream inStream, org.biojava.nbio.genome.io.fastq.FastqVariant variant)
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FastqFileIterator
public FastqFileIterator(java.lang.String fastqFileName)
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FastqFileIterator
public FastqFileIterator(java.lang.String fastqFileName, org.biojava.nbio.genome.io.fastq.FastqVariant variant)
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Method Detail
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close
public void close()
Close file
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getLineNum
public int getLineNum()
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hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfacejava.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
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iterator
public java.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<org.biojava.nbio.genome.io.fastq.Fastq>
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next
public org.biojava.nbio.genome.io.fastq.Fastq next()
- Specified by:
next
in interfacejava.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
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remove
public void remove()
- Specified by:
remove
in interfacejava.util.Iterator<org.biojava.nbio.genome.io.fastq.Fastq>
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