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

Histogram.isEmpty介绍

[英]Returns true if this histogram has no data in in, false otherwise.
[中]

代码示例

代码示例来源：origin: broadinstitute/picard

public boolean areHistogramsEmpty() {
    return (highQualityDepthHistogram.isEmpty() || highQualityDepthHistogramNonZero.isEmpty());
  }
}

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

public boolean areHistogramsEmpty() {
    return (highQualityDepthHistogram.isEmpty() || highQualityDepthHistogramNonZero.isEmpty());
  }
}

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

/**
 * Outputs validation error details to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 *                  processing will stop after this threshold has been reached
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileVerbose(final SamReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  try {
    validateSamFile(samReader, out);
  } catch (MaxOutputExceededException e) {
    out.println("Maximum output of [" + maxVerboseOutput + "] errors reached.");
  }
  final boolean result = errorsByType.isEmpty();
  cleanup();
  return result;
}

代码示例来源：origin: org.seqdoop/htsjdk

/**
 * Outputs validation error details to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 *                  processing will stop after this threshold has been reached
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileVerbose(final SAMFileReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  try {
    validateSamFile(samReader, out);
  } catch (MaxOutputExceededException e) {
    out.println("Maximum output of [" + maxVerboseOutput + "] errors reached.");
  }
  boolean result = errorsByType.isEmpty();
  cleanup();
  return result;
}

代码示例来源：origin: samtools/htsjdk

/**
 * Outputs validation error details to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 *                  processing will stop after this threshold has been reached
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileVerbose(final SamReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  try {
    validateSamFile(samReader, out);
  } catch (MaxOutputExceededException e) {
    out.println("Maximum output of [" + maxVerboseOutput + "] errors reached.");
  }
  final boolean result = errorsByType.isEmpty();
  cleanup();
  return result;
}

代码示例来源：origin: broadinstitute/picard

if (!oqHisto.isEmpty()) metrics.addHistogram(oqHisto);
metrics.write(OUTPUT);
if (qHisto.isEmpty() && oqHisto.isEmpty()) {
  log.warn("No valid bases found in input file. No plot will be produced.");

代码示例来源：origin: broadinstitute/picard

@Override
protected void finish() {
  collector.finish();
  final MetricsFile<RnaSeqMetrics, Integer> file = getMetricsFile();
  collector.addAllLevelsToFile(file);
  file.write(OUTPUT);
  boolean atLeastOneHistogram = false;
  for (final Histogram<Integer> histo : file.getAllHistograms()) {
    atLeastOneHistogram = atLeastOneHistogram || !histo.isEmpty();
  }
  // Generate the coverage by position plot
  if (CHART_OUTPUT != null && atLeastOneHistogram) {
    final int rResult = RExecutor.executeFromClasspath("picard/analysis/rnaSeqCoverage.R",
                              OUTPUT.getAbsolutePath(),
                              CHART_OUTPUT.getAbsolutePath(),
                              INPUT.getName(),
                              this.plotSubtitle);
    if (rResult != 0) {
      throw new PicardException("Problem invoking R to generate plot.");
    }
  }
}

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

@Override
protected void finish() {
  collector.finish();
  final MetricsFile<RnaSeqMetrics, Integer> file = getMetricsFile();
  collector.addAllLevelsToFile(file);
  file.write(OUTPUT);
  boolean atLeastOneHistogram = false;
  for (final Histogram<Integer> histo : file.getAllHistograms()) {
    atLeastOneHistogram = atLeastOneHistogram || !histo.isEmpty();
  }
  // Generate the coverage by position plot
  if (CHART_OUTPUT != null && atLeastOneHistogram) {
    final int rResult = RExecutor.executeFromClasspath("picard/analysis/rnaSeqCoverage.R",
                              OUTPUT.getAbsolutePath(),
                              CHART_OUTPUT.getAbsolutePath(),
                              INPUT.getName(),
                              this.plotSubtitle);
    if (rResult != 0) {
      throw new PicardException("Problem invoking R to generate plot.");
    }
  }
}

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

if (isEmpty()) {
  return;

代码示例来源：origin: samtools/htsjdk

@Test
public void testValidSamFile() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(TEST_DATA_DIR, "valid.sam"));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertTrue(results.isEmpty());
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testValidCRAMFileWithoutSeqDict() throws Exception {
  final File reference = new File(TEST_DATA_DIR, "nm_tag_validation.fa");
  final SamReader samReader = SamReaderFactory
      .makeDefault()
      .validationStringency(ValidationStringency.SILENT)
      .referenceSequence(reference)
      .open(new File(TEST_DATA_DIR, "nm_tag_validation.cram"));
  final Histogram<String> results = executeValidation(samReader,
      new FastaSequenceFile(reference, true),
      IndexValidationStringency.EXHAUSTIVE);
  Assert.assertTrue(!results.isEmpty());
}

代码示例来源：origin: samtools/htsjdk

@Test
public void duplicateReadsOutOfOrder() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(TEST_DATA_DIR, "duplicated_reads_out_of_order.sam"));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertFalse(results.isEmpty());
  Assert.assertEquals(results.get(SAMValidationError.Type.MATES_ARE_SAME_END.getHistogramString()).getValue(), 2.0);
}

代码示例来源：origin: org.seqdoop/htsjdk

private void validateSamFile(final SAMFileReader samReader, final PrintWriter out) {
  try {
    samReader.setValidationStringency(ValidationStringency.SILENT);
    validateHeader(samReader.getFileHeader());
    orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder());
    validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader());
    validateUnmatchedPairs();
    if (validateIndex) {
      try {
        BamIndexValidator.exhaustivelyTestIndex(samReader);
      } catch (Exception e) {
        addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null));
      }
    }
    if (errorsByType.isEmpty()) {
      out.println("No errors found");
    }
  } finally {
    out.flush();
  }
}

代码示例来源：origin: samtools/htsjdk

@Test(enabled = false)
public void duplicateReads() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(TEST_DATA_DIR, "duplicated_reads.sam"));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertFalse(results.isEmpty());
  Assert.assertEquals(results.get(SAMValidationError.Type.MATES_ARE_SAME_END.getHistogramString()).getValue(), 2.0);
}

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

private void validateSamFile(final SamReader samReader, final PrintWriter out) {
  try {
    validateHeader(samReader.getFileHeader());
    orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder());
    validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader());
    validateUnmatchedPairs();
    if (indexValidationStringency != IndexValidationStringency.NONE) {
      try {
        if (indexValidationStringency == IndexValidationStringency.LESS_EXHAUSTIVE) {
          BamIndexValidator.lessExhaustivelyTestIndex(samReader);
        } else {
          BamIndexValidator.exhaustivelyTestIndex(samReader);
        }
      } catch (Exception e) {
        addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null));
      }
    }
    if (errorsByType.isEmpty()) {
      out.println("No errors found");
    }
  } finally {
    out.flush();
  }
}

代码示例来源：origin: samtools/htsjdk

private void validateSamFile(final SamReader samReader, final PrintWriter out) {
  try {
    validateHeader(samReader.getFileHeader());
    orderChecker = new SAMSortOrderChecker(samReader.getFileHeader().getSortOrder());
    validateSamRecordsAndQualityFormat(samReader, samReader.getFileHeader());
    validateUnmatchedPairs();
    if (indexValidationStringency != IndexValidationStringency.NONE) {
      try {
        if (indexValidationStringency == IndexValidationStringency.LESS_EXHAUSTIVE) {
          BamIndexValidator.lessExhaustivelyTestIndex(samReader);
        } else {
          BamIndexValidator.exhaustivelyTestIndex(samReader);
        }
      } catch (Exception e) {
        addError(new SAMValidationError(Type.INVALID_INDEX_FILE_POINTER, e.getMessage(), null));
      }
    }
    if (errorsByType.isEmpty()) {
      out.println("No errors found");
    }
  } finally {
    out.flush();
  }
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testAddHistogram() {
  final int[] is1 = {4,4,5,5,5};
  final Histogram<Integer> histo1 = new Histogram<>();
  Assert.assertTrue(histo1.isEmpty());
  for (final int i : is1) histo1.increment(i);
  Assert.assertFalse(histo1.isEmpty());
  final int[] is2 = {5,5, 6,6,6,6};
  final Histogram<Integer> histo2 = new Histogram<>();
  for (final int i : is2) histo2.increment(i);
  Assert.assertEquals(histo1.get(4).getValue(), 2.0);
  Assert.assertEquals(histo1.get(5).getValue(), 3.0);
  Assert.assertEquals(histo1.get(6), null);
  histo1.addHistogram(histo2);
  Assert.assertEquals(histo1.get(4).getValue(), 2.0);
  Assert.assertEquals(histo1.get(5).getValue(), 5.0);
  Assert.assertEquals(histo1.get(6).getValue(), 4.0);
}

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

/**
 * Outputs validation summary report to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileSummary(final SamReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  validateSamFile(samReader, out);
  boolean result = errorsByType.isEmpty();
  if (errorsByType.getCount() > 0) {
    // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type.
    final Histogram<String> errorsAndWarningsByType = new Histogram<>("Error Type", "Count");
    for (final Histogram.Bin<Type> bin : errorsByType.values()) {
      errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue());
    }
    final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<>();
    errorsByType.setBinLabel("Error Type");
    errorsByType.setValueLabel("Count");
    metricsFile.setHistogram(errorsAndWarningsByType);
    metricsFile.write(out);
  }
  cleanup();
  return result;
}

代码示例来源：origin: samtools/htsjdk

/**
 * Outputs validation summary report to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileSummary(final SamReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  validateSamFile(samReader, out);
  boolean result = errorsByType.isEmpty();
  if (errorsByType.getCount() > 0) {
    // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type.
    final Histogram<String> errorsAndWarningsByType = new Histogram<>("Error Type", "Count");
    for (final Histogram.Bin<Type> bin : errorsByType.values()) {
      errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue());
    }
    final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<>();
    errorsByType.setBinLabel("Error Type");
    errorsByType.setValueLabel("Count");
    metricsFile.setHistogram(errorsAndWarningsByType);
    metricsFile.write(out);
  }
  cleanup();
  return result;
}

代码示例来源：origin: org.seqdoop/htsjdk

/**
 * Outputs validation summary report to out.
 *
 * @param samReader records to validate
 * @param reference if null, NM tag validation is skipped
 * @return boolean  true if there are no validation errors, otherwise false
 */
public boolean validateSamFileSummary(final SAMFileReader samReader, final ReferenceSequenceFile reference) {
  init(reference, samReader.getFileHeader());
  validateSamFile(samReader, out);
  boolean result = errorsByType.isEmpty();
  if (errorsByType.getCount() > 0) {
    // Convert to a histogram with String IDs so that WARNING: or ERROR: can be prepended to the error type.
    final Histogram<String> errorsAndWarningsByType = new Histogram<String>("Error Type", "Count");
    for (final Histogram<SAMValidationError.Type>.Bin bin : errorsByType.values()) {
      errorsAndWarningsByType.increment(bin.getId().getHistogramString(), bin.getValue());
    }
    final MetricsFile<ValidationMetrics, String> metricsFile = new MetricsFile<ValidationMetrics, String>();
    errorsByType.setBinLabel("Error Type");
    errorsByType.setValueLabel("Count");
    metricsFile.setHistogram(errorsAndWarningsByType);
    metricsFile.write(out);
  }
  cleanup();
  return result;
}

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