Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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            args[index++] = "ATTRIBUTE_TO_CLEAR=" + attr;
        }
        runPicardCommandLine(args);

        final SAMFileReader reader = new SAMFileReader(output);
        final SAMFileHeader header = reader.getFileHeader();
        Assert.assertEquals(header.getSortOrder(), SAMFileHeader.SortOrder.queryname);
        Assert.assertEquals(header.getProgramRecords().size(), removeAlignmentInfo ? 0 : 1);
        for (final SAMReadGroupRecord rg : header.getReadGroups()) {
            if (sample != null) {
                Assert.assertEquals(rg.getSample(), sample);
            }
            else {
                Assert.assertEquals(rg.getSample(), "Hi,Mom!");
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    }

    @Test(dataProvider="clipPairedTestData")
    public void testPairedEndClip(final String testName, final String read1, final String read2, final AdapterPair expected) {

        final SAMRecord rec1 = new SAMRecord(new SAMFileHeader());
        rec1.setReadString(read1);
        rec1.setFirstOfPairFlag(true);
        final SAMRecord rec2 = new SAMRecord(new SAMFileHeader());
        rec2.setReadString(read2);
        rec2.setSecondOfPairFlag(true);

        final AdapterPair result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2,
                IlluminaAdapterPair.INDEXED, IlluminaAdapterPair.PAIRED_END);
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    @Test
    public void testAddCommentsToBam() throws Exception {
        final File outputFile = File.createTempFile("addCommentsToBamTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
        runIt(INPUT_FILE, outputFile, commentList);

        final SAMFileHeader newHeader = new SAMFileReader(outputFile).getFileHeader();

        // The original comments are massaged when they're added to the header. Perform the same massaging here,
        // and then compare the lists
        final List<String> massagedComments = new LinkedList<String>();
        for (final String comment : commentList) {
            massagedComments.add(SAMTextHeaderCodec.COMMENT_PREFIX + comment);
        }

        Assert.assertEquals(newHeader.getComments(), massagedComments);
    }
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Related Classes of htsjdk.samtools.SAMFileHeader

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.MergedAlignmentReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.downsampling.FractionalDownsamplerUnitTest$FractionalDownsamplerTest
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