本文整理了Java中htsjdk.samtools.util.Histogram.getMean()
方法的一些代码示例,展示了Histogram.getMean()
的具体用法。这些代码示例主要来源于Github
/Stackoverflow
/Maven
等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。Histogram.getMean()
方法的具体详情如下:
包路径:htsjdk.samtools.util.Histogram
类名称:Histogram
方法名:getMean
[英]Assuming that the key type for the histogram is a Number type, returns the mean of all the items added to the histogram.
[中]假设直方图的键类型是数字类型,则返回添加到直方图的所有项目的平均值。
代码示例来源:origin: com.github.samtools/htsjdk
public double getStandardDeviation() {
final double mean = getMean();
double count = 0;
double total = 0;
for (final Bin<K> bin : map.values()) {
final double localCount = bin.getValue();
final double value = bin.getIdValue();
count += localCount;
total += localCount * pow(value - mean, 2);
}
return Math.sqrt(total / (count-1));
}
代码示例来源:origin: samtools/htsjdk
public double getStandardDeviation() {
final double mean = getMean();
double count = 0;
double total = 0;
for (final Bin<K> bin : map.values()) {
final double localCount = bin.getValue();
final double value = bin.getIdValue();
count += localCount;
total += localCount * pow(value - mean, 2);
}
return Math.sqrt(total / (count-1));
}
代码示例来源:origin: org.seqdoop/htsjdk
public double getStandardDeviation() {
final double mean = getMean();
double count = 0;
double total = 0;
for (final Bin bin : values()) {
final double localCount = bin.getValue();
final double value = bin.getIdValue();
count += localCount;
total += localCount * pow(value - mean, 2);
}
return Math.sqrt(total / (count-1));
}
代码示例来源:origin: broadinstitute/picard
final double averageQuality = qualityHistogram.getMean();
final double standardDeviationQuality = qualityHistogram.getStandardDeviation();
代码示例来源:origin: broadinstitute/picard
public void onComplete() {
//summarize read data
if (metrics.TOTAL_READS > 0)
{
metrics.PCT_PF_READS = (double) metrics.PF_READS / (double) metrics.TOTAL_READS;
metrics.PCT_ADAPTER = this.adapterReads / (double) metrics.PF_READS;
metrics.MEAN_READ_LENGTH = readLengthHistogram.getMean();
//Calculate BAD_CYCLES
metrics.BAD_CYCLES = 0;
for (final Histogram.Bin<Integer> cycleBin : badCycleHistogram.values()) {
final double badCyclePercentage = cycleBin.getValue() / metrics.TOTAL_READS;
if (badCyclePercentage >= 0.8) {
metrics.BAD_CYCLES++;
}
}
if(doRefMetrics) {
if (metrics.PF_READS > 0) metrics.PCT_PF_READS_ALIGNED = (double) metrics.PF_READS_ALIGNED / (double) metrics.PF_READS;
if (metrics.PF_READS_ALIGNED > 0) metrics.PCT_READS_ALIGNED_IN_PAIRS = (double) metrics.READS_ALIGNED_IN_PAIRS / (double) metrics.PF_READS_ALIGNED;
if (metrics.PF_READS_ALIGNED > 0) metrics.PCT_PF_READS_IMPROPER_PAIRS = (double) metrics.PF_READS_IMPROPER_PAIRS / (double) metrics.PF_READS_ALIGNED;
if (metrics.PF_READS_ALIGNED > 0) metrics.STRAND_BALANCE = numPositiveStrand / (double) metrics.PF_READS_ALIGNED;
if (this.chimerasDenominator > 0) metrics.PCT_CHIMERAS = this.chimeras / (double) this.chimerasDenominator;
if (nonBisulfiteAlignedBases > 0) metrics.PF_MISMATCH_RATE = mismatchHistogram.getSum() / (double) nonBisulfiteAlignedBases;
metrics.PF_HQ_MEDIAN_MISMATCHES = hqMismatchHistogram.getMedian();
if (hqNonBisulfiteAlignedBases > 0) metrics.PF_HQ_ERROR_RATE = hqMismatchHistogram.getSum() / (double) hqNonBisulfiteAlignedBases;
if (metrics.PF_ALIGNED_BASES > 0) metrics.PF_INDEL_RATE = this.indels / (double) metrics.PF_ALIGNED_BASES;
}
}
}
代码示例来源:origin: com.github.broadinstitute/picard
public void onComplete() {
//summarize read data
if (metrics.TOTAL_READS > 0)
{
metrics.PCT_PF_READS = (double) metrics.PF_READS / (double) metrics.TOTAL_READS;
metrics.PCT_ADAPTER = this.adapterReads / (double) metrics.PF_READS;
metrics.MEAN_READ_LENGTH = readLengthHistogram.getMean();
//Calculate BAD_CYCLES
metrics.BAD_CYCLES = 0;
for (final Histogram.Bin<Integer> cycleBin : badCycleHistogram.values()) {
final double badCyclePercentage = cycleBin.getValue() / metrics.TOTAL_READS;
if (badCyclePercentage >= 0.8) {
metrics.BAD_CYCLES++;
}
}
if(doRefMetrics) {
if (metrics.PF_READS > 0) metrics.PCT_PF_READS_ALIGNED = (double) metrics.PF_READS_ALIGNED / (double) metrics.PF_READS;
if (metrics.PF_READS_ALIGNED > 0) metrics.PCT_READS_ALIGNED_IN_PAIRS = (double) metrics.READS_ALIGNED_IN_PAIRS / (double) metrics.PF_READS_ALIGNED;
if (metrics.PF_READS_ALIGNED > 0) metrics.PCT_PF_READS_IMPROPER_PAIRS = (double) metrics.PF_READS_IMPROPER_PAIRS / (double) metrics.PF_READS_ALIGNED;
if (metrics.PF_READS_ALIGNED > 0) metrics.STRAND_BALANCE = numPositiveStrand / (double) metrics.PF_READS_ALIGNED;
if (this.chimerasDenominator > 0) metrics.PCT_CHIMERAS = this.chimeras / (double) this.chimerasDenominator;
if (nonBisulfiteAlignedBases > 0) metrics.PF_MISMATCH_RATE = mismatchHistogram.getSum() / (double) nonBisulfiteAlignedBases;
metrics.PF_HQ_MEDIAN_MISMATCHES = hqMismatchHistogram.getMedian();
if (hqNonBisulfiteAlignedBases > 0) metrics.PF_HQ_ERROR_RATE = hqMismatchHistogram.getSum() / (double) hqNonBisulfiteAlignedBases;
if (metrics.PF_ALIGNED_BASES > 0) metrics.PF_INDEL_RATE = this.indels / (double) metrics.PF_ALIGNED_BASES;
}
}
}
代码示例来源:origin: com.github.broadinstitute/picard
final double averageQuality = qualityHistogram.getMean();
final double standardDeviationQuality = qualityHistogram.getStandardDeviation();
代码示例来源:origin: broadinstitute/picard
@Test(dataProvider = "sumOfGaussiansDataProvider")
public void testDrawSumOfQScores(final File metricsFile, final int altDepth, final double tolerance) throws Exception {
final MetricsFile<TheoreticalSensitivityMetrics, Integer> metrics = new MetricsFile<>();
try (final FileReader metricsFileReader = new FileReader(metricsFile)) {
metrics.read(metricsFileReader);
}
final List<Histogram<Integer>> histograms = metrics.getAllHistograms();
final Histogram<Integer> qualityHistogram = histograms.get(1);
final TheoreticalSensitivity.RouletteWheel qualityRW = new TheoreticalSensitivity.RouletteWheel(TheoreticalSensitivity.trimDistribution(TheoreticalSensitivity.normalizeHistogram(qualityHistogram)));
final Random randomNumberGenerator = new Random(51);
// Calculate mean and deviation of quality score distribution to enable Gaussian sampling below
final double averageQuality = qualityHistogram.getMean();
final double standardDeviationQuality = qualityHistogram.getStandardDeviation();
for (int k = 0; k < 1; k++) {
int sumOfQualitiesFull = IntStream.range(0, altDepth).map(n -> qualityRW.draw()).sum();
int sumOfQualities = TheoreticalSensitivity.drawSumOfQScores(altDepth, averageQuality, standardDeviationQuality, randomNumberGenerator.nextGaussian());
Assert.assertEquals(sumOfQualitiesFull, sumOfQualities, sumOfQualitiesFull * tolerance);
}
}
代码示例来源:origin: samtools/htsjdk
@Test(dataProvider = "histogramData")
public void testHistogramFunctions(final int[] values, final double mean, final double stdev, final Integer trimByWidth) {
final Histogram<Integer> histo = new Histogram<>();
for (int value : values) {
histo.increment(value);
}
if (trimByWidth != null) histo.trimByWidth(trimByWidth);
final double m = histo.getMean();
final double sd = histo.getStandardDeviation();
Assert.assertEquals(round(mean), round(m), "Means are not equal");
Assert.assertEquals(round(stdev), round(sd), "Stdevs are not equal");
}
代码示例来源:origin: broadinstitute/picard
metrics.MEAN_INSERT_SIZE = trimmedHistogram.getMean();
metrics.STANDARD_DEVIATION = trimmedHistogram.getStandardDeviation();
代码示例来源:origin: com.github.broadinstitute/picard
metrics.MEAN_INSERT_SIZE = trimmedHistogram.getMean();
metrics.STANDARD_DEVIATION = trimmedHistogram.getStandardDeviation();
代码示例来源:origin: com.github.broadinstitute/picard
metrics.JUMP_LIBRARY_SIZE = (outies > 0 && outieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(outies, outies - outieDupes) : 0;
outieHistogram.trimByTailLimit(TAIL_LIMIT);
metrics.JUMP_MEAN_INSERT_SIZE = outieHistogram.getMean();
metrics.JUMP_STDEV_INSERT_SIZE = outieHistogram.getStandardDeviation();
metrics.NONJUMP_PAIRS = innies;
metrics.NONJUMP_LIBRARY_SIZE = (innies > 0 && innieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(innies, innies - innieDupes) : 0;
innieHistogram.trimByTailLimit(TAIL_LIMIT);
metrics.NONJUMP_MEAN_INSERT_SIZE = innieHistogram.getMean();
metrics.NONJUMP_STDEV_INSERT_SIZE = innieHistogram.getStandardDeviation();
metrics.CHIMERIC_PAIRS = crossChromPairs + superSized + tandemPairs;
代码示例来源:origin: broadinstitute/picard
metrics.JUMP_LIBRARY_SIZE = (outies > 0 && outieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(outies, outies - outieDupes) : 0;
outieHistogram.trimByTailLimit(TAIL_LIMIT);
metrics.JUMP_MEAN_INSERT_SIZE = outieHistogram.getMean();
metrics.JUMP_STDEV_INSERT_SIZE = outieHistogram.getStandardDeviation();
metrics.NONJUMP_PAIRS = innies;
metrics.NONJUMP_LIBRARY_SIZE = (innies > 0 && innieDupes > 0) ? DuplicationMetrics.estimateLibrarySize(innies, innies - innieDupes) : 0;
innieHistogram.trimByTailLimit(TAIL_LIMIT);
metrics.NONJUMP_MEAN_INSERT_SIZE = innieHistogram.getMean();
metrics.NONJUMP_STDEV_INSERT_SIZE = innieHistogram.getStandardDeviation();
metrics.CHIMERIC_PAIRS = crossChromPairs + superSized + tandemPairs;
代码示例来源:origin: com.github.broadinstitute/picard
MEAN_COVERAGE = highQualityDepthHistogram.getMean();
SD_COVERAGE = highQualityDepthHistogram.getStandardDeviation();
MEDIAN_COVERAGE = highQualityDepthHistogram.getMedian();
代码示例来源:origin: broadinstitute/picard
MEAN_COVERAGE = highQualityDepthHistogram.getMean();
SD_COVERAGE = highQualityDepthHistogram.getStandardDeviation();
MEDIAN_COVERAGE = highQualityDepthHistogram.getMedian();
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