本文整理汇总了Java中htsjdk.samtools.util.IOUtil.assertDirectoryIsWritable方法的典型用法代码示例。如果您正苦于以下问题:Java IOUtil.assertDirectoryIsWritable方法的具体用法?Java IOUtil.assertDirectoryIsWritable怎么用?Java IOUtil.assertDirectoryIsWritable使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.IOUtil
的用法示例。
在下文中一共展示了IOUtil.assertDirectoryIsWritable方法的4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,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: onTraversalStart
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
public void onTraversalStart() {
IOUtil.assertDirectoryIsWritable(OUTPUT_DIRECTORY);
if ( readArguments.getReadFiles().size() != 1 ) {
throw new UserException("This tool only accepts a single SAM/BAM/CRAM as input");
}
if (SAMPLE) {
splitters.add(new SampleNameSplitter());
}
if (READ_GROUP) {
splitters.add(new ReadGroupIdSplitter());
}
if (LIBRARY_NAME) {
splitters.add(new LibraryNameSplitter());
}
outs = createWriters(splitters);
}
示例2: assertWritable
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
static void assertWritable(final File output, final boolean outputByReadGroup) {
if (outputByReadGroup) {
if (output != null) {
IOUtil.assertDirectoryIsWritable(output);
}
} else {
IOUtil.assertFileIsWritable(output);
}
}
示例3: doWork
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Override
protected int doWork() {
///////////////////////////////////////////////////////////////////////
// Test and then load up the inputs
///////////////////////////////////////////////////////////////////////
final boolean outputVcfs = VCF_DIR != null;
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsReadable(TRIOS);
IOUtil.assertFileIsWritable(OUTPUT);
if (outputVcfs) IOUtil.assertDirectoryIsWritable(VCF_DIR);
LOG.info("Loading and filtering trios.");
final MendelianViolationDetector.Result result =
VariantProcessor.Builder
.generatingAccumulatorsBy(this::buildDetector)
.withInput(INPUT)
.combiningResultsBy(MendelianViolationDetector.Result::merge)
.multithreadingBy(THREAD_COUNT)
.build()
.process();
// Write out the metrics!
final MetricsFile<MendelianViolationMetrics, ?> metricsFile = getMetricsFile();
for (final MendelianViolationMetrics m : result.metrics()) {
m.calculateDerivedFields();
metricsFile.addMetric(m);
}
metricsFile.write(OUTPUT);
writeAllViolations(result);
return 0;
}
示例4: IndexWriteBean
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@SuppressWarnings("unchecked")
public IndexWriteBean(OptionSet options) {
super();
String[] requiredOPT = {"path"};
VannoUtils.checkMissing(options, requiredOPT);
String path = (String) options.valueOf("path");
IOUtil.assertInputIsValid(path);
this.path = path;
if(options.has("f")) {
format = VannoUtils.parseIndexFileFormat((String)options.valueOf("f"));
} else {
File tbiIndex = new File(path + TabixUtils.STANDARD_INDEX_EXTENSION);
if(tbiIndex.exists()) {
TbiIndex index = new TbiIndex(tbiIndex.getAbsolutePath());
format = index.getFormatWithRef();
}
}
if(format == null) throw new IllegalArgumentException("File format is missing, format can be " + ErrorMsg.INDEX_FILE_FORMAT_CMD);
if(options.has("columns") && format.flag != FormatWithRef.VCF_FORMAT) {
format = VannoUtils.updateFormat(path, format, (List<String>)options.valuesOf("columns"));
}
format.checkOverlap();
if(options.has("comment")) {
String comment = (String)options.valueOf("comment");
if(comment.length() > 1) throw new IllegalArgumentException("metaCharacter should be a char, not " + comment);
format.tbiFormat.metaCharacter = comment.charAt(0);
} else {
format.tbiFormat.metaCharacter = '#';
}
if(options.has("skip")) {
format.tbiFormat.numHeaderLinesToSkip = (Integer)options.valueOf("skip");
} else {
format.tbiFormat.numHeaderLinesToSkip = 0;
}
type = INDEXTYPE.ALL;
if(options.has("t")) type = VannoUtils.checkWriteIndexType((String)options.valueOf("t"));
String pathDir = null;
if(options.has("o")) {
pathDir = (String)options.valueOf("o");
IOUtil.assertDirectoryIsWritable(new File(pathDir));
}
if(pathDir == null) {
outputPathPlus = path + BinIndexWriter.PLUS_EXTENSION;
outputPathPlusIndex = path + BinIndexWriter.PLUS_INDEX_EXTENSION;
} else {
if(type == INDEXTYPE.PLUS_INDEX) {
outputPathPlus = path + BinIndexWriter.PLUS_EXTENSION;
IOUtil.assertInputIsValid(outputPathPlus);
} else {
outputPathPlus = pathDir + new File(path).getName() + BinIndexWriter.PLUS_EXTENSION;
}
outputPathPlusIndex = pathDir + new File(path).getName() + BinIndexWriter.PLUS_INDEX_EXTENSION;
}
}