Examples of addPair()

Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        // Create some alignments that hit the ribosomal sequence, various parts of the gene, and intergenic.
        final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate);
        // Set seed so that strandedness is consistent among runs.
        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);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate);
        // Set seed so that strandedness is consistent among runs.
        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);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        // Set seed so that strandedness is consistent among runs.
        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);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        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");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
        final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("2");
        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");
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("2");
        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");
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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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);
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Examples of htsjdk.samtools.SAMRecordSetBuilder.addPair()

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        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");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
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Examples of org.apache.camel.component.splunk.event.SplunkEvent.addPair()

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    @Override
    public void process(Exchange exchange) throws Exception {
        SplunkEvent splunkEvent = new SplunkEvent();

        splunkEvent.addPair("ERRORKEY", "AVUA123");
        splunkEvent.addPair("ERRORMSG", "Service ABC Failed");
        splunkEvent.addPair("ERRORDESC", "BusinessException: Username and password don't match");
        splunkEvent.addPair(SplunkEvent.COMMON_START_TIME, "Thu Aug 15 2014 00:15:06");

        exchange.getIn().setBody(splunkEvent, SplunkEvent.class);
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Examples of org.apache.camel.component.splunk.event.SplunkEvent.addPair()

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    @Override
    public void process(Exchange exchange) throws Exception {
        SplunkEvent splunkEvent = new SplunkEvent();

        splunkEvent.addPair("ERRORKEY", "AVUA123");
        splunkEvent.addPair("ERRORMSG", "Service ABC Failed");
        splunkEvent.addPair("ERRORDESC", "BusinessException: Username and password don't match");
        splunkEvent.addPair(SplunkEvent.COMMON_START_TIME, "Thu Aug 15 2014 00:15:06");

        exchange.getIn().setBody(splunkEvent, SplunkEvent.class);
    }
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