htsjdk.samtools.util.Histogram.getMedian()方法的使用及代码示例

x33g5p2x  于2022-01-20 转载在 其他  
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本文整理了Java中htsjdk.samtools.util.Histogram.getMedian()方法的一些代码示例，展示了Histogram.getMedian()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.getMedian()方法的具体详情如下：
包路径：htsjdk.samtools.util.Histogram
类名称：Histogram
方法名：getMedian

Histogram.getMedian介绍

[英]Gets the median absolute deviation of the distribution.
[中]获取分布的中位数绝对偏差。

代码示例

代码示例来源：origin: samtools/htsjdk

/** Gets the median absolute deviation of the distribution. */
public double getMedianAbsoluteDeviation() {
  final double median = getMedian();
  final Histogram<Double> deviations = new Histogram<>();
  for (final Bin<K> bin : values()) {
    final double dev = abs(bin.getIdValue() - median);
    deviations.increment(dev, bin.getValue());
  }
  return deviations.getMedian();
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testMad() {
  final int[] is = {4,4,4,4,5,5,5,5,6,6,6,6,6,6,7,7,7,7,7,7,7,8,8,8,8,8,8,8,8};
  final Histogram<Integer> histo = new Histogram<>();
  for (final int i : is) histo.increment(i);
  Assert.assertEquals(7d, histo.getMedian());
  Assert.assertEquals(1d, histo.getMedianAbsoluteDeviation());
  Assert.assertTrue(abs(histo.estimateSdViaMad() - 1.4826) < 0.0001);
}

代码示例来源：origin: broadinstitute/picard

metrics.MAX_INSERT_SIZE = (int) histogram.getMax();
metrics.MIN_INSERT_SIZE = (int) histogram.getMin();
metrics.MEDIAN_INSERT_SIZE = histogram.getMedian();
metrics.MODE_INSERT_SIZE = histogram.getMode();
metrics.MEDIAN_ABSOLUTE_DEVIATION = histogram.getMedianAbsoluteDeviation();
final double median = histogram.getMedian();
double covered = 0;
double low = median;

代码示例来源：origin: com.github.samtools/htsjdk

/** Gets the median absolute deviation of the distribution. */
public double getMedianAbsoluteDeviation() {
  final double median = getMedian();
  final Histogram<Double> deviations = new Histogram<>();
  for (final Bin<K> bin : values()) {
    final double dev = abs(bin.getIdValue() - median);
    deviations.increment(dev, bin.getValue());
  }
  return deviations.getMedian();
}

代码示例来源：origin: com.github.broadinstitute/picard

metrics.MAX_INSERT_SIZE = (int) histogram.getMax();
metrics.MIN_INSERT_SIZE = (int) histogram.getMin();
metrics.MEDIAN_INSERT_SIZE = histogram.getMedian();
metrics.MODE_INSERT_SIZE = histogram.getMode();
metrics.MEDIAN_ABSOLUTE_DEVIATION = histogram.getMedianAbsoluteDeviation();
final double median = histogram.getMedian();
double covered = 0;
double low = median;

代码示例来源：origin: org.seqdoop/htsjdk

/** Gets the median absolute deviation of the distribution. */
public double getMedianAbsoluteDeviation() {
  final double median = getMedian();
  final Histogram<Double> deviations = new Histogram<Double>();
  for (final Bin bin : values()) {
    final double dev = abs(bin.getIdValue() - median);
    deviations.increment(dev, bin.getValue());
  }
  return deviations.getMedian();
}

代码示例来源：origin: broadinstitute/picard

MEAN_COVERAGE    = highQualityDepthHistogram.getMean();
SD_COVERAGE      = highQualityDepthHistogram.getStandardDeviation();
MEDIAN_COVERAGE  = highQualityDepthHistogram.getMedian();
MAD_COVERAGE     = highQualityDepthHistogram.getMedianAbsoluteDeviation();

代码示例来源：origin: samtools/htsjdk

@Test(dataProvider = "medianTestData")
public void testMedian(final int [] values, final double median) {
  final Histogram<Integer> histo = new Histogram<>();
  for (final int i : values) histo.increment(i);
  Assert.assertEquals(histo.getMedian(), median);
}

代码示例来源：origin: com.github.broadinstitute/picard

MEAN_COVERAGE    = highQualityDepthHistogram.getMean();
SD_COVERAGE      = highQualityDepthHistogram.getStandardDeviation();
MEDIAN_COVERAGE  = highQualityDepthHistogram.getMedian();
MAD_COVERAGE     = highQualityDepthHistogram.getMedianAbsoluteDeviation();

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: broadinstitute/picard

this.metrics.MEDIAN_CV_COVERAGE = cvs.getMedian();
this.metrics.MEDIAN_5PRIME_BIAS = fivePrimeSkews.getMedian();
this.metrics.MEDIAN_3PRIME_BIAS = threePrimeSkews.getMedian();
this.metrics.MEDIAN_5PRIME_TO_3PRIME_BIAS = fiveToThreeSkews.getMedian();

代码示例来源：origin: com.github.broadinstitute/picard

this.metrics.MEDIAN_CV_COVERAGE = cvs.getMedian();
this.metrics.MEDIAN_5PRIME_BIAS = fivePrimeSkews.getMedian();
this.metrics.MEDIAN_3PRIME_BIAS = threePrimeSkews.getMedian();
this.metrics.MEDIAN_5PRIME_TO_3PRIME_BIAS = fiveToThreeSkews.getMedian();

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;
    }
  }
}

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