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java.lang.Objectedu.unc.csbio.RNASim.QualityGenerator
edu.unc.csbio.RNASim.RealQualityGenerator
public class RealQualityGenerator
The class RealQualityGenerator
extending
QualityGenerator
is for generating quality score from real fq
files.
Field Summary | |
---|---|
private java.io.BufferedReader |
br1
two BufferedReader to read two fq files |
private java.io.BufferedReader |
br2
two BufferedReader to read two fq files |
private java.lang.String |
fq1
location of two fq files |
private java.lang.String |
fq2
location of two fq files |
private boolean |
isQualityScoreFound
to check whether quality score is found |
Constructor Summary | |
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RealQualityGenerator(java.lang.String _fq1,
java.lang.String _fq2)
this is the constructor for object RealQualityGenerator |
Method Summary | |
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java.lang.String[] |
generate(Read[] r)
Generate read quality score by sampling real Fastq file. |
private void |
ResetBufferReader()
this method reset BufferReader br1 and br2 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private java.io.BufferedReader br1
private java.io.BufferedReader br2
private java.lang.String fq1
private java.lang.String fq2
private boolean isQualityScoreFound
Constructor Detail |
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public RealQualityGenerator(java.lang.String _fq1, java.lang.String _fq2) throws java.io.IOException
RealQualityGenerator
_fq1
- location of first fq file_fq2
- location of second fq file
java.io.IOException
- if an input or output exception occurredMethod Detail |
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private void ResetBufferReader() throws java.io.IOException
br1
and br2
java.io.IOException
- if an input or output exception occurredpublic java.lang.String[] generate(Read[] r) throws java.lang.RuntimeException
generate
in class QualityGenerator
r
- an array of read
there
- is not enough lines in real Fastq file
java.lang.RuntimeException
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