本文整理汇总了Java中htsjdk.samtools.util.IOUtil.assertInputIsValid方法的典型用法代码示例。如果您正苦于以下问题:Java IOUtil.assertInputIsValid方法的具体用法?Java IOUtil.assertInputIsValid怎么用?Java IOUtil.assertInputIsValid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.assertInputIsValid方法的11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: AbstractVCFParser
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public AbstractVCFParser(final FormatWithRef format, final String path) {
super(format);
this.codec = new VCFCodec();
IOUtil.assertInputIsValid(path);
readHeaderFiles(new File(path));
}
示例2: outVCFHeader
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public VCFHeader outVCFHeader() {
try {
if(vcfHeaderPath == null) {
System.out.println("*** Note: Your output format is vcf, you should define header-path for vcf header or we won't output header.");
return null;
} else {
IOUtil.assertInputIsValid(vcfHeaderPath);
return (VCFHeader)(new VCFCodec()).readActualHeader(new LineIteratorImpl(new File(vcfHeaderPath)));
}
} catch (FileNotFoundException e) {
e.printStackTrace();
}
return null;
}
示例3: setQueryFile
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setQueryFile(String queryFile) {
IOUtil.assertInputIsValid(queryFile);
this.queryFile = queryFile;
}
示例4: setFieldsFormat
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setFieldsFormat(String fieldsFormat) {
IOUtil.assertInputIsValid(fieldsFormat);
this.fieldsFormat = fieldsFormat;
}
示例5: setFieldVcfInfo
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setFieldVcfInfo(String fieldVcfInfo) {
IOUtil.assertInputIsValid(fieldVcfInfo);
this.fieldVcfInfo = fieldVcfInfo;
}
示例6: 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;
}
}
示例7: setOverlapFile
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setOverlapFile(String overlapFile) {
IOUtil.assertInputIsValid(overlapFile);
this.overlapFile = overlapFile;
}
示例8: setHeaderPath
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setHeaderPath(String headerPath) {
IOUtil.assertInputIsValid(headerPath);
this.headerPath = headerPath;
}
示例9: setAnnoConfig
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setAnnoConfig(String annoConfig) {
IOUtil.assertInputIsValid(annoConfig);
this.annoConfig = annoConfig;
}
示例10: setDb
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
public void setDb(String dbPath) {
IOUtil.assertInputIsValid(dbPath);
this.db = dbPath;
}
示例11: doWork
import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
protected int doWork() {
IOUtil.assertInputIsValid(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
final SamReader in = SamReaderFactory.makeDefault()
.referenceSequence(REFERENCE_SEQUENCE)
.open(SamInputResource.of(INPUT));
// create the read-group we'll be using
final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
rg.setLibrary(RGLB);
rg.setPlatform(RGPL);
rg.setSample(RGSM);
rg.setPlatformUnit(RGPU);
if (RGCN != null) rg.setSequencingCenter(RGCN);
if (RGDS != null) rg.setDescription(RGDS);
if (RGDT != null) rg.setRunDate(RGDT);
if (RGPI != null) rg.setPredictedMedianInsertSize(RGPI);
if (RGPG != null) rg.setProgramGroup(RGPG);
if (RGPM != null) rg.setPlatformModel(RGPM);
if (RGKS != null) rg.setKeySequence(RGKS);
if (RGFO != null) rg.setFlowOrder(RGFO);
log.info(String.format("Created read-group ID=%s PL=%s LB=%s SM=%s%n", rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));
// create the new header and output file
final SAMFileHeader inHeader = in.getFileHeader();
final SAMFileHeader outHeader = inHeader.clone();
outHeader.setReadGroups(Collections.singletonList(rg));
if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);
final SAMFileWriter outWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader,
outHeader.getSortOrder() == inHeader.getSortOrder(),
OUTPUT);
final ProgressLogger progress = new ProgressLogger(log);
for (final SAMRecord read : in) {
read.setAttribute(SAMTag.RG.name(), RGID);
outWriter.addAlignment(read);
progress.record(read);
}
// cleanup
CloserUtil.close(in);
outWriter.close();
return 0;
}