Examples of addRowID()

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

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        } else {
            argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2);
        }
        argumentsTable.addColumn("Argument");
        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
        argumentsTable.addRowID("covariate", true);
        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        }
        argumentsTable.addColumn("Argument");
        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
        argumentsTable.addRowID("covariate", true);
        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
        argumentsTable.addRowID("solid_recal_mode", true);
        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME);
        argumentsTable.addRowID("covariate", true);
        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
        argumentsTable.addRowID("solid_recal_mode", true);
        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
        argumentsTable.addRowID("solid_nocall_strategy", true);
        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
        argumentsTable.addRowID("no_standard_covs", true);
        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
        argumentsTable.addRowID("solid_recal_mode", true);
        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
        argumentsTable.addRowID("solid_nocall_strategy", true);
        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
        argumentsTable.addRowID("mismatches_context_size", true);
        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
        argumentsTable.addRowID("run_without_dbsnp", true);
        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
        argumentsTable.addRowID("solid_recal_mode", true);
        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
        argumentsTable.addRowID("solid_nocall_strategy", true);
        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
        argumentsTable.addRowID("mismatches_context_size", true);
        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
        argumentsTable.addRowID("indels_context_size", true);
        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
        argumentsTable.addRowID("solid_recal_mode", true);
        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
        argumentsTable.addRowID("solid_nocall_strategy", true);
        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
        argumentsTable.addRowID("mismatches_context_size", true);
        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
        argumentsTable.addRowID("indels_context_size", true);
        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
        argumentsTable.addRowID("mismatches_default_quality", true);
        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
        argumentsTable.addRowID("solid_nocall_strategy", true);
        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
        argumentsTable.addRowID("mismatches_context_size", true);
        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
        argumentsTable.addRowID("indels_context_size", true);
        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
        argumentsTable.addRowID("mismatches_default_quality", true);
        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
        argumentsTable.addRowID("deletions_default_quality", true);
        argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
        argumentsTable.addRowID("mismatches_context_size", true);
        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
        argumentsTable.addRowID("indels_context_size", true);
        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
        argumentsTable.addRowID("mismatches_default_quality", true);
        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
        argumentsTable.addRowID("deletions_default_quality", true);
        argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
        argumentsTable.addRowID("insertions_default_quality", true);
        argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
        argumentsTable.addRowID("indels_context_size", true);
        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
        argumentsTable.addRowID("mismatches_default_quality", true);
        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
        argumentsTable.addRowID("deletions_default_quality", true);
        argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
        argumentsTable.addRowID("insertions_default_quality", true);
        argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
        argumentsTable.addRowID("maximum_cycle_value", true);
        argumentsTable.set("maximum_cycle_value", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MAXIMUM_CYCLE_VALUE);
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Examples of org.broadinstitute.gatk.engine.report.GATKReportTable.addRowID()

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        argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
        argumentsTable.addRowID("mismatches_default_quality", true);
        argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
        argumentsTable.addRowID("deletions_default_quality", true);
        argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
        argumentsTable.addRowID("insertions_default_quality", true);
        argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
        argumentsTable.addRowID("maximum_cycle_value", true);
        argumentsTable.set("maximum_cycle_value", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MAXIMUM_CYCLE_VALUE);
        argumentsTable.addRowID("low_quality_tail", true);
        argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL);
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