Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.IntervalList

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        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();

        // Create an interval list with one ribosomal interval.
        final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
        final IntervalList rRnaIntervalList = new IntervalList(builder.getHeader());
        rRnaIntervalList.add(rRnaInterval);
        final File rRnaIntervalsFile = File.createTempFile("tmp.rRna.", ".interval_list");
        rRnaIntervalsFile.deleteOnExit();
        rRnaIntervalList.write(rRnaIntervalsFile);

        // Generate the metrics.
        final File metricsFile = File.createTempFile("tmp.", ".rna_metrics");

        final String[] args = new String[] {
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        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();

        // Create an interval list with one ribosomal interval.
        final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
        final IntervalList rRnaIntervalList = new IntervalList(builder.getHeader());
        rRnaIntervalList.add(rRnaInterval);
        final File rRnaIntervalsFile = File.createTempFile("tmp.rRna.", ".interval_list");
        rRnaIntervalsFile.deleteOnExit();
        rRnaIntervalList.write(rRnaIntervalsFile);

        // Generate the metrics.
        final File metricsFile = File.createTempFile("tmp.", ".rna_metrics");

        final String[] args = new String[] {
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        final List<IntervalList> scatter = scatterer.scatter(tc.source, tc.scatterWidth);
        Assert.assertEquals(scatter, tc.expectedScatter);
    }
   
    private static IntervalList composeIntervalList(final IntervalList source, final String chromosome, final int... segmentsByPair) {
        final IntervalList intervals = new IntervalList(source.getHeader());
        for (int i = 0; i < segmentsByPair.length; i += 2) {
            final Interval parentInterval = lookupIntervalContainingLocus(source, chromosome, segmentsByPair[i]);
            intervals.add(new Interval("1", segmentsByPair[i], segmentsByPair[i + 1], parentInterval.isNegativeStrand(), parentInterval.getName()));
        }
        return intervals;
    }
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Related Classes of htsjdk.samtools.util.IntervalList

  • org.broadinstitute.gatk.utils.interval.IntervalUtils
  • org.broadinstitute.gatk.utils.interval.IntervalUtilsUnitTest
  • picard.analysis.CollectOxoGMetrics
  • picard.analysis.CollectRnaSeqMetricsTest
  • picard.analysis.directed.CollectTargetedMetrics
  • picard.analysis.directed.RnaSeqMetricsCollector
  • picard.illumina.CollectIlluminaSummaryMetrics
  • picard.reference.ExtractSequences
  • picard.util.BaitDesigner
  • picard.util.BedToIntervalList
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