public class ArtificialFastqGenerationUtils
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.util.Random |
randNumGenerator |
Constructor and Description |
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ArtificialFastqGenerationUtils() |
Modifier and Type | Method and Description |
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static int |
calculateTargetCoverageFromGCcontent(double GCcontent)
Deprecated.
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static double |
generateRandomDoubleBetween0And1()
Generates a random double between 0 and 1.
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static char[] |
getAlternateGenotypes(char genotype)
Return a char array containing the alternate genotypes.
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static int |
getRandomIntWithinRange(int mean,
double standardDeviation,
int minimum,
int maximum)
Generates a pseudo-random number from a normal distribution, but with a minimum and maximum value.
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static java.lang.String |
getStackTraceString(java.lang.Exception e)
Generate a stack trace string for an exception object.
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static int |
getTargetCoverageViaGaussFuncOfGCcont(double GCcontent,
double coverageMeanPeak,
double coverageMeanPeakGCcontent,
double coverageMeanGCcontentSpread,
double coverageSDdividedByMean)
This method calculates a region's target coverage from its GC content.
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static boolean |
isACGT(char genotype)
Check if a genotype (represented as a char) is A/C/G/T.
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static boolean |
isGC(char genotype)
Check if a genotype (represented as a char) is G/C.
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static <T extends AbstractRead> |
setRedundantReadToNull(T redundantRead)
Set the sequence field of Read and BabyRead objects to null and then also set the object to null.
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public static boolean isACGT(char genotype)
genotype
- - the genotype whose type we are checking.public static boolean isGC(char genotype)
genotype
- - the genotype whose type we are checking.public static char[] getAlternateGenotypes(char genotype)
genotype
- - genotype for which we want the alternatives.public static int getRandomIntWithinRange(int mean, double standardDeviation, int minimum, int maximum)
mean
- - the population mean.standardDeviation
- - the population standard deviation.minimum
- - the minimum possible value.maximum
- - the maximum possible value.public static int getTargetCoverageViaGaussFuncOfGCcont(double GCcontent, double coverageMeanPeak, double coverageMeanPeakGCcontent, double coverageMeanGCcontentSpread, double coverageSDdividedByMean)
GCcontent
- coverageMeanPeak
- coverageMeanPeakGCcontent
- coverageMeanGCcontentSpread
- coverageSDdividedByMean
- public static double generateRandomDoubleBetween0And1()
public static java.lang.String getStackTraceString(java.lang.Exception e)
e
- - the exception object.public static <T extends AbstractRead> void setRedundantReadToNull(T redundantRead)
redundantRead
- @Deprecated public static int calculateTargetCoverageFromGCcontent(double GCcontent)