public GATKReportTable generateReportTable(final String covariateNames) {
GATKReportTable argumentsTable;
if (SORT_BY_ALL_COLUMNS) {
argumentsTable =
new GATKReportTable(
"Arguments",
"Recalibration argument collection values used in this run",
2,
GATKReportTable.TableSortingWay.SORT_BY_COLUMN);
} 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);
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);
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);
argumentsTable.addRowID("default_platform", true);
argumentsTable.set("default_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM);
argumentsTable.addRowID("force_platform", true);
argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
argumentsTable.addRowID("quantizing_levels", true);
argumentsTable.set(
"quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
argumentsTable.addRowID("recalibration_report", true);
argumentsTable.set(
"recalibration_report",
RecalUtils.ARGUMENT_VALUE_COLUMN_NAME,
existingRecalibrationReport == null
? "null"
: existingRecalibrationReport.getAbsolutePath());
argumentsTable.addRowID("binary_tag_name", true);
argumentsTable.set(
"binary_tag_name",
RecalUtils.ARGUMENT_VALUE_COLUMN_NAME,
BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME);
return argumentsTable;
}
