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java.lang.Objectedu.unc.csbio.RNASim.ReadModifier
public class ReadModifier
The class modifies pair-end reads from a sequence.
Field Summary | |
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private static char[] |
whole
all possible nucleotides as a char array |
Constructor Summary | |
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ReadModifier()
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Method Summary | |
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private static char |
change(char original,
double errorProb)
the method to change original nucleotide based on given error probability |
static int |
modify(Read[] r,
java.lang.String[] qs)
a method to change read sequence based on given quality score For each char, qs[i], in the array, Qphred = qs[i] - 64. |
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 static char[] whole
Constructor Detail |
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public ReadModifier()
Method Detail |
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private static char change(char original, double errorProb)
original
- nucleotideerrorProb
- the error probability
public static int modify(Read[] r, java.lang.String[] qs) throws java.lang.RuntimeException
r
- read sequenceqs
- an array of encoded Phred scores
java.lang.RuntimeException
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