本文整理汇总了Java中htsjdk.samtools.metrics.MetricsFile类的典型用法代码示例。如果您正苦于以下问题:Java MetricsFile类的具体用法?Java MetricsFile怎么用?Java MetricsFile使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
MetricsFile类属于htsjdk.samtools.metrics包,在下文中一共展示了MetricsFile类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: testBasicScoring
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Note that (due to raw data), this test includes collapsing over libraries (not just the contexts).
* @throws IOException
*/
@Test
public void testBasicScoring() throws IOException {
final MetricsFile<SequencingArtifactMetrics.PreAdapterDetailMetrics, Comparable<?>> mf = new MetricsFile<>();
mf.read(new FileReader(testPreAdapterDetailsMetrics));
final Map<Transition, Double> scoreMap = PreAdapterOrientationScorer.scoreOrientationBiasMetricsOverContext(mf.getMetrics());
Assert.assertNotNull(scoreMap);
Assert.assertEquals(scoreMap.keySet().size(), 12);
// Ground truth values painstakingly derived manually
Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'C')), 100.0, 1e-6);
Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'G')), 50.5788416297570, 1e-6);
Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'T')), 100.0, 1e-6);
Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'A')), 100.0, 1e-6);
Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'G')), 100.0, 1e-6);
Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'T')), 58.0641821538479, 1e-6);
}
开发者ID:broadinstitute,项目名称:gatk-protected,代码行数:23,代码来源:PreAdapterOrientationScorerUnitTest.java
示例2: testBasicCounting
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Note that (due to raw data), this test includes collapsing over libraries (not just the contexts).
* @throws IOException
*/
@Test
public void testBasicCounting() throws IOException {
final MetricsFile<SequencingArtifactMetrics.PreAdapterDetailMetrics, Comparable<?>> mf = new MetricsFile<>();
mf.read(new FileReader(testPreAdapterDetailsMetrics));
final Map<Transition, RealMatrix> countMap = PreAdapterOrientationScorer.countOrientationBiasMetricsOverContext(mf.getMetrics());
Assert.assertNotNull(countMap);
Assert.assertEquals(countMap.keySet().size(), 12);
// Ground truth values painstakingly derived manually from both libraries (hence four values in the expression instead of two)
// L1 norm can be used since all values are always positive.
Assert.assertEquals(countMap.get(Transition.transitionOf('A', 'C')).getRowVector(0).getL1Norm(), 2836660 + 2631203 + 240 + 246, 1e-1);
Assert.assertEquals(countMap.get(Transition.transitionOf('A', 'C')).getRowVector(1).getL1Norm(), 2852491 + 333 + 2646654 + 297, 1e-1);
Assert.assertEquals(countMap.get(Transition.transitionOf('A', 'G')).getRowVector(0).getL1Norm(), 2631203 + 416 + 2836660 + 481, 1e-1);
Assert.assertEquals(countMap.get(Transition.transitionOf('A', 'G')).getRowVector(1).getL1Norm(), 2852491 + 404 + 2646654 + 397, 1e-1);
}
开发者ID:broadinstitute,项目名称:gatk-protected,代码行数:22,代码来源:PreAdapterOrientationScorerUnitTest.java
示例3: getMatcherStatMetrics
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Gets the accumulated statistics for barcodes match/mismatch.
*
* Note: calling this method recomputes the percentage every time.
*
* @see MatcherStat
*/
public MetricsFile<MatcherStat, Integer> getMatcherStatMetrics() {
// create the matcher stats
final MetricsFile<MatcherStat, Integer> matcherStats = new MetricsFile<>();
// add the header and the metrics
matcherStats.addHeader(metricHeader);
// update the percentage value
final double total = stats.values().stream().mapToInt(i -> i.RECORDS).sum();
// for each value, set the percentage and add the metric
stats.values().forEach(ms -> {
ms.PCT_RECORDS = 100d * ms.RECORDS / total;
matcherStats.addMetric(ms);
});
return matcherStats;
}
开发者ID:magicDGS,项目名称:ReadTools,代码行数:23,代码来源:BarcodeDecoder.java
示例4: getBarcodeStatMetrics
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Gets the accumulated statistics for each barcode.
*
* @see BarcodeStat
*/
public MetricsFile<BarcodeStat, Integer> getBarcodeStatMetrics() {
// create the barcode stats
final MetricsFile<BarcodeStat, Integer> barcode = new MetricsFile<>();
for (int i = 0; i < dictionary.getNumberOfBarcodes(); i++) {
final Map<String, BarcodeStat> current = barcodeStats.get(i);
for (final Map.Entry<String, Histogram<Integer>> entry : mismatchesHist.get(i)
.entrySet()) {
final BarcodeStat s = current.get(entry.getKey());
s.MEAN_MISMATCH = entry.getValue().getMean();
s.MEAN_N = nMean.get(i).get(entry.getKey()).mean();
barcode.addHistogram(entry.getValue());
}
barcode.addAllMetrics(current.values());
}
return barcode;
}
开发者ID:magicDGS,项目名称:ReadTools,代码行数:22,代码来源:BarcodeDecoder.java
示例5: onTraversalSuccess
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Prints the statistics for each barcode into a metrics file and logs the number of records
* per barcode.
*/
@Override
public Object onTraversalSuccess() {
// TODO: maybe we should create a metric file per statistic
final Path path = outputBamArgumentCollection.makeMetricsFile(null);
try (final Writer metricsWriter = Files.newBufferedWriter(path)) {
// trimer metrics with the header
final MetricsFile<TrimmerMetric, Integer> trimming = getMetricsFile();
trimming.addAllMetrics(pipeline.getTrimmingStats());
trimming.write(metricsWriter);
// filter metrics with histogram without header
final MetricsFile<FilterMetric, Integer> filtering = new MetricsFile<>();
filtering.addAllMetrics(pipeline.getFilterStats());
lengthHistogramsBeforeTrimming.forEach(filtering::addHistogram);
lengthHistogramsAfterTrimming.forEach(filtering::addHistogram);
filtering.write(metricsWriter);
} catch (IOException e) {
throw new UserException.CouldNotCreateOutputFile(path.toString(), e.getMessage(), e);
}
return null;
}
开发者ID:magicDGS,项目名称:ReadTools,代码行数:27,代码来源:TrimReads.java
示例6: testZeroLengthReads
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Test
public void testZeroLengthReads() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test2.sam");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
// test that it doesn't blow up
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:18,代码来源:CollectAlignmentSummaryMetricsTest.java
示例7: onComplete
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Handles completion of metric collection. Metrics are computed from counts of data and written out to a file.
*/
private void onComplete() {
try {
final MetricsFile<IlluminaBasecallingMetrics, Comparable<?>> file = getMetricsFile();
final IlluminaMetricCounts allLaneCounts = new IlluminaMetricCounts(null, null, LANE);
for (final String s : barcodeToMetricCounts.keySet()) {
final IlluminaMetricCounts counts = barcodeToMetricCounts.get(s);
counts.addMetricsToFile(file);
allLaneCounts.addIlluminaMetricCounts(counts);
}
if (!barcodeToMetricCounts.keySet().contains("")) {
allLaneCounts.addMetricsToFile(file); // detect non-indexed case
}
file.write(OUTPUT);
} catch (final Exception ex) {
throw new PicardException("Error writing output file " + OUTPUT.getPath(), ex);
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:21,代码来源:CollectIlluminaBasecallingMetrics.java
示例8: outputDetailMetricsFile
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Outputs the detailed statistics tables for SNP and Indel match categories.
**/
public static void outputDetailMetricsFile(final VariantContext.Type variantType, final MetricsFile<GenotypeConcordanceDetailMetrics,?> genotypeConcordanceDetailMetricsFile,
final GenotypeConcordanceCounts counter, final String truthSampleName, final String callSampleName,
final boolean missingSitesHomRef, final boolean outputAllRows) {
final GenotypeConcordanceSchemeFactory schemeFactory = new GenotypeConcordanceSchemeFactory();
final GenotypeConcordanceScheme scheme = schemeFactory.getScheme(missingSitesHomRef);
scheme.validateScheme();
for (final TruthState truthState : TruthState.values()) {
for (final CallState callState : CallState.values()) {
final long count = counter.getCount(truthState, callState);
final String contingencyValues = scheme.getContingencyStateString(truthState, callState);
if (count > 0 || outputAllRows) {
final GenotypeConcordanceDetailMetrics detailMetrics = new GenotypeConcordanceDetailMetrics();
detailMetrics.VARIANT_TYPE = variantType;
detailMetrics.TRUTH_SAMPLE = truthSampleName;
detailMetrics.CALL_SAMPLE = callSampleName;
detailMetrics.TRUTH_STATE = truthState;
detailMetrics.CALL_STATE = callState;
detailMetrics.COUNT = count;
detailMetrics.CONTINGENCY_VALUES = contingencyValues;
genotypeConcordanceDetailMetricsFile.addMetric(detailMetrics);
}
}
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:28,代码来源:GenotypeConcordance.java
示例9: doWork
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
if(OUTPUT != null) IOUtil.assertFileIsWritable(OUTPUT);
final MetricsFile<CrosscheckMetric, ?> metricsFile = getMetricsFile();
try {
metricsFile.read(new FileReader(INPUT));
} catch (FileNotFoundException e) {
e.printStackTrace();
return 1;
}
clusterMetrics(metricsFile.getMetrics()).write(OUTPUT);
return 0;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:19,代码来源:ClusterCrosscheckMetrics.java
示例10: finish
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Override
protected void finish() {
final MetricsFile<BaseDistributionByCycleMetrics, ?> metrics = getMetricsFile();
hist.addToMetricsFile(metrics);
metrics.write(OUTPUT);
if (hist.isEmpty()) {
log.warn("No valid bases found in input file. No plot will be produced.");
} else {
final int rResult = RExecutor.executeFromClasspath("picard/analysis/baseDistributionByCycle.R",
OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
INPUT.getName(),
plotSubtitle);
if (rResult != 0) {
throw new PicardException("R script nucleotideDistributionByCycle.R failed with return code " + rResult);
}
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:19,代码来源:CollectBaseDistributionByCycle.java
示例11: saveResults
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
protected void saveResults(final MetricsFile<?, Integer> metrics, final SAMFileHeader readsHeader, final String inputFileName) {
MetricsUtils.saveMetrics(metrics, out);
if (metrics.getAllHistograms().isEmpty()) {
logger.warn("No valid bases found in input file.");
} else if (chartOutput != null) {
// Now run R to generate a chart
// If we're working with a single library, assign that library's name
// as a suffix to the plot title
final List<SAMReadGroupRecord> readGroups = readsHeader.getReadGroups();
/*
* A subtitle for the plot, usually corresponding to a library.
*/
String plotSubtitle = "";
if (readGroups.size() == 1) {
plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
}
final RScriptExecutor executor = new RScriptExecutor();
executor.addScript(getBaseDistributionByCycleRScriptResource());
executor.addArgs(out, chartOutput.getAbsolutePath(), inputFileName, plotSubtitle);
executor.exec();
}
}
开发者ID:broadinstitute,项目名称:gatk,代码行数:26,代码来源:CollectBaseDistributionByCycleSpark.java
示例12: writeResultsToFiles
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
private void writeResultsToFiles() {
final MetricsFile<GcBiasMetrics, Integer> file = getMetricsFile();
final MetricsFile<GcBiasDetailMetrics, ?> detailMetricsFile = getMetricsFile();
final MetricsFile<GcBiasSummaryMetrics, ?> summaryMetricsFile = getMetricsFile();
multiCollector.addAllLevelsToFile(file);
final List<GcBiasMetrics> gcBiasMetricsList = file.getMetrics();
for (final GcBiasMetrics gcbm : gcBiasMetricsList) {
final List<GcBiasDetailMetrics> gcDetailList = gcbm.DETAILS.getMetrics();
for (final GcBiasDetailMetrics d : gcDetailList) {
detailMetricsFile.addMetric(d);
}
summaryMetricsFile.addMetric(gcbm.SUMMARY);
}
detailMetricsFile.write(OUTPUT);
summaryMetricsFile.write(SUMMARY_OUTPUT);
final NumberFormat fmt = NumberFormat.getIntegerInstance();
fmt.setGroupingUsed(true);
RExecutor.executeFromClasspath(R_SCRIPT,
OUTPUT.getAbsolutePath(),
SUMMARY_OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
String.valueOf(SCAN_WINDOW_SIZE));
}
开发者ID:broadinstitute,项目名称:picard,代码行数:25,代码来源:CollectGcBiasMetrics.java
示例13: doWork
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Override
protected int doWork() {
IOUtil.assertFilesAreReadable(metricsFiles);
final MetricsFile<?, ?> metricsA = new MetricsFile();
final MetricsFile<?, ?> metricsB = new MetricsFile();
try {
metricsA.read(new FileReader(metricsFiles.get(0)));
metricsB.read(new FileReader(metricsFiles.get(1)));
final boolean areEqual = metricsA.areMetricsEqual(metricsB) && metricsA.areHistogramsEqual(metricsB);
final String status = areEqual ? "EQUAL" : "NOT EQUAL";
log.info("Files " + metricsFiles.get(0) + " and " + metricsFiles.get(1) + "are " + status);
} catch (final Exception e) {
throw new PicardException(e.getMessage());
}
return 0;
}
开发者ID:broadinstitute,项目名称:picard,代码行数:17,代码来源:CompareMetrics.java
示例14: testChimeras
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Test
public void testChimeras() throws IOException {
final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test_chimeras.sam");
final File reference = new File(TEST_DATA_DIR, "summary_alignment_stats_test.fasta");
final File outfile = File.createTempFile("alignmentMetrics", ".txt");
outfile.deleteOnExit();
final String[] args = new String[] {
"INPUT=" + input.getAbsolutePath(),
"OUTPUT=" + outfile.getAbsolutePath(),
"MAX_INSERT_SIZE=20",
"REFERENCE_SEQUENCE=" + reference.getAbsolutePath(),
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<>();
output.read(new FileReader(outfile));
for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
if (metrics.CATEGORY == AlignmentSummaryMetrics.Category.FIRST_OF_PAIR) {
TestNGUtil.compareDoubleWithAccuracy(metrics.PCT_CHIMERAS, 5D / 6, 0.0001);
}
if (metrics.CATEGORY == AlignmentSummaryMetrics.Category.SECOND_OF_PAIR) {
TestNGUtil.compareDoubleWithAccuracy(metrics.PCT_CHIMERAS, 3D / 6, 0.0001);
}
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:27,代码来源:CollectAlignmentSummaryMetricsTest.java
示例15: finish
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Override
protected void finish() {
// Generate a "Histogram" of mean quality and write it to the file
final MetricsFile<?,Integer> metrics = getMetricsFile();
metrics.addHistogram(q.getMeanQualityHistogram());
if (!oq.isEmpty()) metrics.addHistogram(oq.getMeanQualityHistogram());
metrics.write(OUTPUT);
if (q.isEmpty() && oq.isEmpty()) {
log.warn("No valid bases found in input file. No plot will be produced.");
}
else {
// Now run R to generate a chart
final int rResult = RExecutor.executeFromClasspath(
"picard/analysis/meanQualityByCycle.R",
OUTPUT.getAbsolutePath(),
CHART_OUTPUT.getAbsolutePath(),
INPUT.getName(),
plotSubtitle);
if (rResult != 0) {
throw new PicardException("R script meanQualityByCycle.R failed with return code " + rResult);
}
}
}
开发者ID:broadinstitute,项目名称:picard,代码行数:26,代码来源:MeanQualityByCycle.java
示例16: saveMetricsRDD
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
/**
* Saves the metrics to a file.
* Note: the SamFileHeader is needed in order to include libraries that didn't have any duplicates.
* @param result metrics object, potentially pre-initialized with headers,
*/
public static void saveMetricsRDD(final MetricsFile<DuplicationMetrics, Double> result, final SAMFileHeader header, final JavaPairRDD<String, DuplicationMetrics> metricsRDD, final String metricsOutputPath) {
final LibraryIdGenerator libraryIdGenerator = new LibraryIdGenerator(header);
final Map<String, DuplicationMetrics> nonEmptyMetricsByLibrary = metricsRDD.collectAsMap(); //Unknown Library
final Map<String, DuplicationMetrics> emptyMapByLibrary = libraryIdGenerator.getMetricsByLibraryMap();//with null
final List<String> sortedListOfLibraryNames = new ArrayList<>(Sets.union(emptyMapByLibrary.keySet(), nonEmptyMetricsByLibrary.keySet()));
sortedListOfLibraryNames.sort(Utils.COMPARE_STRINGS_NULLS_FIRST);
for (final String library : sortedListOfLibraryNames){
//if a non-empty exists, take it, otherwise take from the the empties. This is done to include libraries with zero data in them.
//But not all libraries are listed in the header (esp in testing data) so we union empty and non-empty
final DuplicationMetrics metricsToAdd = nonEmptyMetricsByLibrary.containsKey(library) ? nonEmptyMetricsByLibrary.get(library) : emptyMapByLibrary.get(library);
metricsToAdd.calculateDerivedMetrics();
result.addMetric(metricsToAdd);
}
if (nonEmptyMetricsByLibrary.size() == 1) {
result.setHistogram(nonEmptyMetricsByLibrary.values().iterator().next().calculateRoiHistogram());
}
MetricsUtils.saveMetrics(result, metricsOutputPath);
}
开发者ID:broadinstitute,项目名称:gatk,代码行数:28,代码来源:MarkDuplicatesSparkUtils.java
示例17: testSaveMetrics
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Test(dataProvider = "metricsPaths", groups = "bucket")
public void testSaveMetrics(String destinationPrefix) throws IOException {
final String outputPath = BucketUtils.getTempFilePath(destinationPrefix, ".txt");
TestMetric testMetric = new TestMetric();
testMetric.value1 = 10;
testMetric.value2 = 5;
final MetricsFile<TestMetric, ?> metrics = new MetricsFile<>();
metrics.addMetric(testMetric);
MetricsUtils.saveMetrics(metrics, outputPath);
Assert.assertTrue(BucketUtils.fileExists(outputPath));
File localCopy = copyFileToLocalTmpFile(outputPath);
final File expectedMetrics = createTempFile("expectedMetrics", ".txt");
metrics.write(expectedMetrics);
Assert.assertTrue(MetricsFile.areMetricsEqual(localCopy, expectedMetrics));
}
开发者ID:broadinstitute,项目名称:gatk,代码行数:19,代码来源:MetricsUtilsTest.java
示例18: saveResults
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
private void saveResults(final MetricsFile<?, Integer> metrics, final SAMFileHeader readsHeader, final String inputFileName){
MetricsUtils.saveMetrics(metrics, out);
if (metrics.getAllHistograms().isEmpty()) {
logger.warn("No valid bases found in input file.");
} else if (chartOutput != null){
// Now run R to generate a chart
// If we're working with a single library, assign that library's name
// as a suffix to the plot title
final List<SAMReadGroupRecord> readGroups = readsHeader.getReadGroups();
/*
* A subtitle for the plot, usually corresponding to a library.
*/
String plotSubtitle = "";
if (readGroups.size() == 1) {
plotSubtitle = StringUtil.asEmptyIfNull(readGroups.get(0).getLibrary());
}
final RScriptExecutor executor = new RScriptExecutor();
executor.addScript(getMeanQualityByCycleRScriptResource());
executor.addArgs(out, chartOutput.getAbsolutePath(), inputFileName, plotSubtitle);
executor.exec();
}
}
开发者ID:broadinstitute,项目名称:gatk,代码行数:26,代码来源:MeanQualityByCycleSpark.java
示例19: testNoLocsSymlink
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
@Test
public void testNoLocsSymlink() throws Exception {
final File metricsFile = File.createTempFile("dual.", ".metrics");
metricsFile.deleteOnExit();
final String[] args = new String[]{
"BASECALLS_DIR=" + noSymlink.getAbsolutePath(),
"LANE=" + 1,
"METRICS_FILE=" + metricsFile,
"READ_STRUCTURE=" + "25T8B8B25T",
"BARCODE=" + "CAATAGTCCGACTCTC"
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> result = new MetricsFile<>();
result.read(new FileReader(metricsFile));
Assert.assertEquals(result.getMetrics().get(0).PERFECT_MATCHES, 2, "Got wrong number of perfect matches");
Assert.assertEquals(result.getMetrics().get(0).ONE_MISMATCH_MATCHES, 0, "Got wrong number of one-mismatch matches");
}
开发者ID:broadinstitute,项目名称:picard,代码行数:20,代码来源:ExtractIlluminaBarcodesTest.java
示例20: runIt
import htsjdk.samtools.metrics.MetricsFile; //导入依赖的package包/类
private MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> runIt(final int lane, final String readStructure)
throws Exception {
final File metricsFile = File.createTempFile("eib.", ".metrics");
metricsFile.deleteOnExit();
final List<String> args = new ArrayList<>(Arrays.asList(
"BASECALLS_DIR=" + basecallsDir.getPath(),
"LANE=" + lane,
"READ_STRUCTURE=" + readStructure,
"METRICS_FILE=" + metricsFile.getPath()
));
for (final String barcode : BARCODES) {
args.add("BARCODE=" + barcode);
}
return runIt(args, metricsFile);
}
开发者ID:broadinstitute,项目名称:picard,代码行数:17,代码来源:ExtractIlluminaBarcodesTest.java
注:本文中的htsjdk.samtools.metrics.MetricsFile类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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