Package org.broadinstitute.gatk.engine.report

Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addColumn()

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        table.addColumn("readgroup");
        //* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
        //* median read length for each read group in every BAM file.
        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
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        table.addColumn("readgroup");
        //* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
        //* median read length for each read group in every BAM file.
        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
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        //* Emits a GATKReport containing read group, sample, library, platform, center, median insert size and
        //* median read length for each read group in every BAM file.
        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
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        //* median read length for each read group in every BAM file.
        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
View Full Code Here
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        table.addColumn("sample", "%s");
        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");
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        table.addColumn("library", "%s");
        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");
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        table.addColumn("platform", "%s");
        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");

        for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
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        table.addColumn("center", "%s");
        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");

        for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
            final String rgID = rg.getId();
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        table.addColumn("date", "%s");
        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");

        for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
            final String rgID = rg.getId();
            table.addRowID(rgID, true);
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        table.addColumn("has.any.reads");
        table.addColumn("is.paired.end");
        table.addColumn("n.reads.analyzed", "%d");
        table.addColumn("simple.read.type", "%s");
        table.addColumn("median.read.length");
        table.addColumn("median.insert.size");

        for ( final SAMReadGroupRecord rg : getToolkit().getSAMFileHeader().getReadGroups() ) {
            final String rgID = rg.getId();
            table.addRowID(rgID, true);
            PerReadGroupInfo info = readGroupInfo.get(rgID);
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