本文整理汇总了Java中htsjdk.samtools.SAMReadGroupRecord.setDescription方法的典型用法代码示例。如果您正苦于以下问题:Java SAMReadGroupRecord.setDescription方法的具体用法?Java SAMReadGroupRecord.setDescription怎么用?Java SAMReadGroupRecord.setDescription使用的例子?那么, 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.SAMReadGroupRecord
的用法示例。
在下文中一共展示了SAMReadGroupRecord.setDescription方法的3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: createReadGroupRecord
import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
protected SAMReadGroupRecord createReadGroupRecord(
String RGID, String RGLB, String RGPL,
String RGPU, String RGSM, String RGCN,
String RGDS, Iso8601Date RGDT, Integer RGPI) {
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);
return rg;
}
示例2: createSamFileHeader
import htsjdk.samtools.SAMReadGroupRecord; //导入方法依赖的package包/类
/** Creates a simple header with the values provided on the command line. */
public SAMFileHeader createSamFileHeader() {
final SAMReadGroupRecord rgroup = new SAMReadGroupRecord(this.READ_GROUP_NAME);
rgroup.setSample(this.SAMPLE_NAME);
if (this.LIBRARY_NAME != null) rgroup.setLibrary(this.LIBRARY_NAME);
if (this.PLATFORM != null) rgroup.setPlatform(this.PLATFORM);
if (this.PLATFORM_UNIT != null) rgroup.setPlatformUnit(this.PLATFORM_UNIT);
if (this.SEQUENCING_CENTER != null) rgroup.setSequencingCenter(SEQUENCING_CENTER);
if (this.PREDICTED_INSERT_SIZE != null) rgroup.setPredictedMedianInsertSize(PREDICTED_INSERT_SIZE);
if (this.DESCRIPTION != null) rgroup.setDescription(this.DESCRIPTION);
if (this.RUN_DATE != null) rgroup.setRunDate(this.RUN_DATE);
if (this.PLATFORM_MODEL != null) rgroup.setPlatformModel(this.PLATFORM_MODEL);
if (this.PROGRAM_GROUP != null) rgroup.setProgramGroup(this.PROGRAM_GROUP);
final SAMFileHeader header = new SAMFileHeader();
header.addReadGroup(rgroup);
for (final String comment : COMMENT) {
header.addComment(comment);
}
header.setSortOrder(this.SORT_ORDER);
return header ;
}
示例3: doWork
import htsjdk.samtools.SAMReadGroupRecord; //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;
}