public class TheoreticalSensitivity
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
TheoreticalSensitivity.RouletteWheel |
Constructor and Description |
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TheoreticalSensitivity() |
Modifier and Type | Method and Description |
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static java.util.List<java.util.ArrayList<java.lang.Double>> |
hetAltDepthDistribution(int N) |
static double |
hetSNPSensitivity(double[] depthDistribution,
double[] qualityDistribution,
int sampleSize,
double logOddsThreshold) |
static double |
hetSNPSensitivity(double[] depthDistribution,
double[] qualityDistribution,
int sampleSize,
double logOddsThreshold,
boolean withLogging) |
static double[] |
normalizeHistogram(htsjdk.samtools.util.Histogram<java.lang.Integer> histogram) |
static java.util.List<java.util.ArrayList<java.lang.Double>> |
proportionsAboveThresholds(java.util.List<java.util.ArrayList<java.lang.Integer>> lists,
java.util.List<java.lang.Double> thresholds) |
public static double hetSNPSensitivity(double[] depthDistribution, double[] qualityDistribution, int sampleSize, double logOddsThreshold)
depthDistribution
- the probability of depth n is depthDistribution[n] for n = 0, 1. . . N - 1qualityDistribution
- the probability of quality q is qualityDistribution[q] for q = 0, 1. . . QsampleSize
- sample size is the number of random sums of quality scores for each mlogOddsThreshold
- is the log_10 of the likelihood ratio required to call a SNP,
for example 5 if the variant likelihood must be 10^5 times greaterpublic static double hetSNPSensitivity(double[] depthDistribution, double[] qualityDistribution, int sampleSize, double logOddsThreshold, boolean withLogging)
depthDistribution
- the probability of depth n is depthDistribution[n] for n = 0, 1. . . N - 1qualityDistribution
- the probability of quality q is qualityDistribution[q] for q = 0, 1. . . QsampleSize
- sample size is the number of random sums of quality scores for each mlogOddsThreshold
- is the log_10 of the likelihood ratio required to call a SNP,
for example 5 if the variant likelihood must be 10^5 times greater.withLogging
- true to output log messages, false otherwise.public static java.util.List<java.util.ArrayList<java.lang.Double>> proportionsAboveThresholds(java.util.List<java.util.ArrayList<java.lang.Integer>> lists, java.util.List<java.lang.Double> thresholds)
public static java.util.List<java.util.ArrayList<java.lang.Double>> hetAltDepthDistribution(int N)
public static double[] normalizeHistogram(htsjdk.samtools.util.Histogram<java.lang.Integer> histogram)