htsjdk.samtools.util.Histogram.getSum()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.getSum()方法的一些代码示例，展示了Histogram.getSum()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.getSum()方法的具体详情如下：
包路径：htsjdk.samtools.util.Histogram
类名称：Histogram
方法名：getSum

Histogram.getSum介绍

[英]Returns the sum of the products of the histgram bin ids and the number of entries in each bin. Note: This is only supported if this histogram stores instances of Number.
[中]返回组织结构图bin ID的乘积和每个bin中的条目数之和。注意：仅当此直方图存储数字的实例时，才支持此操作。

代码示例

代码示例来源：origin: org.seqdoop/htsjdk

public double getMean() {
  if (mean == null) {
    mean = getSum() / getCount();
  }
  return mean;
}

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: samtools/htsjdk

@Test
public void testGetSum() {
  final int[] is = {4,4,5,5,5};
  final Histogram<Integer> histo = new Histogram<>();
  for (final int i : is) histo.increment(i);
  Assert.assertEquals(histo.getSum(), (double)(2*4+3*5), 0.000001);
}

代码示例来源：origin: samtools/htsjdk

@Test(expectedExceptions = UnsupportedOperationException.class)
public void testGetSumBlowup() {
  final String[] is = {"foo", "foo", "bar"};
  final Histogram<String> histo = new Histogram<>();
  for (final String i : is) histo.increment(i);
  histo.getSum();//blow up
}

代码示例来源：origin: broadinstitute/picard

final long thisMetricTotal        = (long) highQualityDepthHistogram.getSum();
final long otherMetricTotal       = (long) otherMetric.highQualityDepthHistogram.getSum();
final long total                  = thisMetricTotal + otherMetricTotal;
final long thisTotalWithExcludes  = (long) (thisMetricTotal / (1.0 - PCT_EXC_TOTAL));

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

final long thisMetricTotal        = (long) highQualityDepthHistogram.getSum();
final long otherMetricTotal       = (long) otherMetric.highQualityDepthHistogram.getSum();
final long total                  = thisMetricTotal + otherMetricTotal;
final long thisTotalWithExcludes  = (long) (thisMetricTotal / (1.0 - PCT_EXC_TOTAL));

代码示例来源：origin: broadinstitute/picard

/** Metrics for evaluating the performance of whole genome sequencing experiments. */
public static class WgsMetrics extends MergeableMetricBase {
  /** The intervals over which this metric was computed. */
  @MergingIsManual
  protected IntervalList intervals;
  /** Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY (default 20) */
  @MergingIsManual
  protected final Histogram<Integer> highQualityDepthHistogram;
  /** Count of sites with a given depth of coverage. Includes all but quality 2 bases */
  @MergingIsManual
  protected final Histogram<Integer> unfilteredDepthHistogram;
  /** The count of bases observed with a given base quality. */
  @MergingIsManual
  protected final Histogram<Integer> unfilteredBaseQHistogram;
  /** The maximum depth/coverage to consider. */
  @MergeByAssertEquals
  protected final int coverageCap;
  /** The sample size used for theoretical het sensitivity. */
  @NoMergingKeepsValue
  protected final int theoreticalHetSensitivitySampleSize;
  /**
   * Create an instance of this metric that is not mergeable.
   */

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

/** Metrics for evaluating the performance of whole genome sequencing experiments. */
public static class WgsMetrics extends MergeableMetricBase {
  /** The intervals over which this metric was computed. */
  @MergingIsManual
  protected IntervalList intervals;
  /** Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY (default 20) */
  @MergingIsManual
  protected final Histogram<Integer> highQualityDepthHistogram;
  /** Count of sites with a given depth of coverage. Includes all but quality 2 bases */
  @MergingIsManual
  protected final Histogram<Integer> unfilteredDepthHistogram;
  /** The count of bases observed with a given base quality. */
  @MergingIsManual
  protected final Histogram<Integer> unfilteredBaseQHistogram;
  /** The maximum depth/coverage to consider. */
  @MergeByAssertEquals
  protected final int coverageCap;
  /** The sample size used for theoretical het sensitivity. */
  @NoMergingKeepsValue
  protected final int theoreticalHetSensitivitySampleSize;
  /**
   * Create an instance of this metric that is not mergeable.
   */

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