Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileReader

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        };
    }

    @Test(dataProvider = "variedAccumulationLevels")
    public void multilevelCollectorTest(final Set<MetricAccumulationLevel> accumulationLevels) {
        final SAMFileReader in = new SAMFileReader(TESTFILE);
        final RecordCountMultiLevelCollector collector = new RecordCountMultiLevelCollector(accumulationLevels, in.getFileHeader().getReadGroups());

        for (final SAMRecord rec : in) {
            collector.acceptRecord(rec, null);
        }
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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) {
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Related Classes of htsjdk.samtools.SAMFileReader

  • org.broad.igv.cli_plugin.AlignmentDecoder
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broad.igv.sam.reader.SAMFileGroup$SamGroupIterator
  • org.broad.igv.sam.reader.SAMReader
  • org.broad.igv.sam.SAMWriterTest
  • org.broadinstitute.gatk.engine.CommandLineGATKUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndexUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.PicardBaselineBenchmark
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