Java Code Examples for htsjdk.samtools.SAMReadGroupRecord#setRunDate()
The following examples show how to use
htsjdk.samtools.SAMReadGroupRecord#setRunDate() .
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Example 1
Source File: FastqToSam.java From picard with MIT License | 6 votes |
/** 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 ; }
Example 2
Source File: HalvadeReducer.java From halvade with GNU General Public License v3.0 | 6 votes |
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; }
Example 3
Source File: AddOrReplaceReadGroups.java From picard with MIT License | 4 votes |
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; }