Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader.addReadGroup()

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    @Test()
    public void testPLFromReadWithRGButNoPL() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final String rgID = "ID";
        final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
        header.addReadGroup(rg);
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
        read.setAttribute("RG", rgID);
        Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
    }
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            final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("rg" + i);
            final String sample = "sample" + i;
            samples.add(sample);
            rg.setSample(sample);
            rg.setPlatform(NGSPlatform.ILLUMINA.getDefaultPlatform());
            header.addReadGroup(rg);
        }

        final boolean downsample = downsampleTo != -1;
        final DownsamplingMethod downsampler = downsample
                ? new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsampleTo, null)
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                rg.setSample(SAMPLE_ALIAS);
            }
            if (LIBRARY_NAME != null) {
                rg.setLibrary(LIBRARY_NAME);
            }
            outHeader.addReadGroup(rg);
        }
        outHeader.setSortOrder(SORT_ORDER);
        if (!REMOVE_ALIGNMENT_INFORMATION) {
            outHeader.setSequenceDictionary(inHeader.getSequenceDictionary());
            outHeader.setProgramRecords(inHeader.getProgramRecords());
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        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);

        final SAMFileHeader header = new SAMFileHeader();
        header.addReadGroup(rgroup);

        for (final String comment : COMMENT) {
            header.addComment(comment);
        }
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            }
        }

        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);
        header.addReadGroup(rg);
        return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output));
    }

    public static void main(final String[] args) {
        System.exit(new IlluminaBasecallsToSam().instanceMain(args));
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                    libraryToRg.put(lib, new ArrayList<SAMReadGroupRecord>());
                }
                libraryToRg.get(lib).add(rg);
            }
            else {
                unknownHeader.addReadGroup(rg);
            }
        }

        if (libraryToRg.size() == 0) {
            log.error("No individual libraries are " +
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