Examples of addFrag()

Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        builder.setRandomSeed(0);
        final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        rg1.setSample("Sample");
        rg1.setLibrary("foo");
        builder.setReadGroup(rg1);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);

        final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
        rg2.setSample("Sample");
        rg2.setLibrary("bar");
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        rg1.setLibrary("foo");
        builder.setReadGroup(rg1);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);

        final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
        rg2.setSample("Sample");
        rg2.setLibrary("bar");
        builder.setReadGroup(rg2);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
        rg2.setSample("Sample");
        rg2.setLibrary("bar");
        builder.setReadGroup(rg2);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addFrag()

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        builder.setReadGroup(rg2);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();
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