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

Histogram.get介绍

[英]Retrieves the bin associated with the given key.
[中]检索与给定密钥关联的bin。

代码示例

代码示例来源：origin: broadinstitute/picard

/**
 * Returns the count defined by the truth state set and call state set.
 */
public long getCount(final TruthAndCallStates truthAndCallStates) {
  final Histogram.Bin<TruthAndCallStates> bin = this.counter.get(truthAndCallStates);
  return (bin == null ? 0L : (long) bin.getValue());
}

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

public static double[] normalizeHistogram(final Histogram<Integer> histogram) {
  if (histogram == null) throw new PicardException("Histogram is null and cannot be normalized");
  final double histogramSumOfValues = histogram.getSumOfValues();
  final double[] normalizedHistogram = new double[histogram.size()];
  for (int i = 0; i < histogram.size(); i++) {
    if (histogram.get(i) != null) {
      normalizedHistogram[i] = histogram.get(i).getValue() / histogramSumOfValues;
    }
  }
  return normalizedHistogram;
}

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

/**
 * Returns the count defined by the truth state set and call state set.
 */
public long getCount(final TruthAndCallStates truthAndCallStates) {
  final Histogram.Bin<TruthAndCallStates> bin = this.counter.get(truthAndCallStates);
  return (bin == null ? 0L : (long) bin.getValue());
}

代码示例来源：origin: broadinstitute/picard

public static double[] normalizeHistogram(final Histogram<Integer> histogram) {
  if (histogram == null) throw new PicardException("Histogram is null and cannot be normalized");
  final double histogramSumOfValues = histogram.getSumOfValues();
  final double[] normalizedHistogram = new double[histogram.size()];
  for (int i = 0; i < histogram.size(); i++) {
    if (histogram.get(i) != null) {
      normalizedHistogram[i] = histogram.get(i).getValue() / histogramSumOfValues;
    }
  }
  return normalizedHistogram;
}

代码示例来源：origin: org.seqdoop/htsjdk

/** Increments the value in the designated bin by the supplied increment. */
public void increment(final K id, final double increment) {
  Bin bin = get(id);
  if (bin == null) {
    bin = new Bin(id);
    put(id, bin);
  }
  bin.value += increment;
  mean = null;
}

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

/***
 * Mutable method that allows the addition of a Histogram into the current one.
 * @param addHistogram
 */
public void addHistogram(final Histogram<K> addHistogram) {
  for (final K key : addHistogram.keySet()){
    this.increment(key, addHistogram.get(key).getValue());
  }
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testLabelsAndComparator() {
  final String[] is = {"a", "B", "a"};
  final Histogram<String> histo = new Histogram<>("FOO", "BAR", String.CASE_INSENSITIVE_ORDER);
  for (final String i : is) histo.increment(i);
  Assert.assertEquals(histo.get("a").getValue(), 2.0);
  Assert.assertEquals(histo.get("B").getValue(), 1.0);
  Assert.assertEquals(histo.get("a").getId(), "a");
  Assert.assertEquals(histo.get("B").getId(), "B");
}

代码示例来源：origin: samtools/htsjdk

@Test(dataProvider = "testMateCigarScenarios")
public void testMateCigarScenarios(final String scenario, final String inputFile, final SAMValidationError.Type expectedError)
    throws Exception {
  final SamReader reader = SamReaderFactory.makeDefault().open(new File(TEST_DATA_DIR, inputFile));
  final Histogram<String> results = executeValidation(reader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertNotNull(results.get(expectedError.getHistogramString()), scenario);
  Assert.assertEquals(results.get(expectedError.getHistogramString()).getValue(), 1.0, scenario);
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testHeaderValidation() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT)
      .open(new File(TEST_DATA_DIR, "buggyHeader.sam"));
  final File referenceFile = new File(TEST_DATA_DIR, "../hg19mini.fasta");
  final ReferenceSequenceFile reference = new FastaSequenceFile(referenceFile, false);
  final Histogram<String> results = executeValidation(samReader, reference, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.UNRECOGNIZED_HEADER_TYPE.getHistogramString()).getValue(), 3.0);
  Assert.assertEquals(results.get(SAMValidationError.Type.HEADER_TAG_MULTIPLY_DEFINED.getHistogramString()).getValue(), 1.0);
  Assert.assertEquals(results.get(SAMValidationError.Type.MISMATCH_FILE_SEQ_DICT.getHistogramString()).getValue(), 1.0);
}

代码示例来源：origin: samtools/htsjdk

@Test(dataProvider = "validateBamFileTerminationData")
public void validateBamFileTerminationTest(final File file, final SAMValidationError.Type errorType, final int numWarnings, final int numErrors) throws IOException {
  final SamFileValidator samFileValidator = new SamFileValidator(new PrintWriter(System.out), 8000);
  samFileValidator.validateBamFileTermination(file);
  Assert.assertEquals(samFileValidator.getErrorsByType().get(errorType).getValue(), 1.0);
  Assert.assertEquals(samFileValidator.getNumWarnings(), numWarnings);
  Assert.assertEquals(samFileValidator.getNumErrors(), numErrors);
}

代码示例来源：origin: samtools/htsjdk

@Test(enabled = false, description = "File is actually valid for Standard quality scores so this test fails with an NPE.")
public void testQualityFormatValidation() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().open(new File("./src/test/resources/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam"));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  final Histogram.Bin<String> bin = results.get(SAMValidationError.Type.INVALID_QUALITY_FORMAT.getHistogramString());
  final double value = bin.getValue();
  Assert.assertEquals(value, 1.0);
}

代码示例来源：origin: samtools/htsjdk

@Test(dataProvider = "missingMateTestCases")
public void testMissingMate(final SAMFileHeader.SortOrder sortOrder) throws IOException {
  final SAMRecordSetBuilder samBuilder = new SAMRecordSetBuilder(true, sortOrder);
  samBuilder.addPair(String.valueOf(1), 1, 1, 101);
  final Iterator<SAMRecord> records = samBuilder.iterator();
  records.next();
  records.remove();
  final Histogram<String> results = executeValidation(samBuilder.getSamReader(), null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.MATE_NOT_FOUND.getHistogramString()).getValue(), 1.0);
}

代码示例来源：origin: samtools/htsjdk

@Test(dataProvider = "testQualitiesNotStored")
public void testNotStoredQualitiesFields(final String inputFile, final double expectedValue) throws IOException {
  try (final SamReader reader = SamReaderFactory.makeDefault().open((new File(TEST_DATA_DIR, inputFile)))) {
    final Histogram<String> results = executeValidation(reader, null, IndexValidationStringency.EXHAUSTIVE);
    Assert.assertEquals(results.get(SAMValidationError.Type.QUALITY_NOT_STORED.getHistogramString()).getValue(), expectedValue);
  }
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testDuplicateRGIDs() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT)
      .open((new File(TEST_DATA_DIR, "duplicate_rg.sam")));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.DUPLICATE_READ_GROUP_ID.getHistogramString()).getValue(), 1.0);
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testIndexFileValidation() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT)
      .enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES).open((new File(TEST_DATA_DIR, "bad_index.bam")));
  Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.INVALID_INDEX_FILE_POINTER.getHistogramString()).getValue(), 1.0);
  results = executeValidation(samReader, null, IndexValidationStringency.LESS_EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.INVALID_INDEX_FILE_POINTER.getHistogramString()).getValue(), 1.0);
}

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: samtools/htsjdk

@Test
public void testPlatformInvalid() throws Exception {
  final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT)
      .open((new File(TEST_DATA_DIR, "invalid_platform_unit.sam")));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.INVALID_PLATFORM_VALUE.getHistogramString()).getValue(), 1.0);
}

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: samtools/htsjdk

@Test
public void testHeaderVersionValidation() throws Exception {
  final String header = "@HD	VN:Hi,Mom!	SO:queryname";
  final InputStream strm = new ByteArrayInputStream(StringUtil.stringToBytes(header));
  final SamReader samReader = SamReaderFactory.makeDefault().open(SamInputResource.of(strm));
  final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertEquals(results.get(SAMValidationError.Type.INVALID_VERSION_NUMBER.getHistogramString()).getValue(), 1.0);
}

代码示例来源：origin: samtools/htsjdk

@Test
public void testCigarNoSeqValidation() throws Exception {
  final SAMRecordSetBuilder samBuilder = new SAMRecordSetBuilder();
  samBuilder.addFrag("name", 0, 1, false);
  samBuilder.iterator().next().setReadBases(SAMRecord.NULL_SEQUENCE);
  samBuilder.iterator().next().setBaseQualities(SAMRecord.NULL_SEQUENCE);
  final Histogram<String> results = executeValidation(samBuilder.getSamReader(), null, IndexValidationStringency.EXHAUSTIVE);
  Assert.assertNull(results.get(SAMValidationError.Type.MISMATCH_CIGAR_SEQ_LENGTH .getHistogramString()));
}

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