diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java index 80e8b574a..876ce585a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java @@ -170,7 +170,7 @@ public class RecalDataManager { final ArrayList requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates ArrayList optionalCovariates = new ArrayList(); - if (argumentCollection.USE_STANDARD_COVARIATES) + if (!argumentCollection.DO_NOT_USE_STANDARD_COVARIATES) optionalCovariates = addStandardCovariatesToList(standardClasses); // add the standard covariates if -standard was specified by the user if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified @@ -180,7 +180,7 @@ public class RecalDataManager { if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class foundClass = true; if (!requiredClasses.contains(covClass) && - (!argumentCollection.USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { + (argumentCollection.DO_NOT_USE_STANDARD_COVARIATES || !standardClasses.contains(covClass))) { try { final Covariate covariate = covClass.newInstance(); // now that we've found a matching class, try to instantiate it optionalCovariates.add(covariate); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index 22b26317b..2688fe655 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -71,16 +71,19 @@ public class RecalibrationArgumentCollection { public boolean LIST_ONLY = false; /** - * Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you. See the list of covariates with -list. + * Note that the ReadGroup and QualityScore covariates are required and do not need to be specified. + * Also, unless --no_standard_covs is specified, the Cycle and Context covariates are standard and are included by default. + * Use the --list argument to see the available covariates. */ - @Argument(fullName = "covariate", shortName = "cov", doc = "Covariates to be used in the recalibration. Each covariate is given as a separate cov parameter. ReadGroup and ReportedQuality are required covariates and are already added for you.", required = false) + @Argument(fullName = "covariate", shortName = "cov", doc = "One or more covariates to be used in the recalibration. Can be specified multiple times", required = false) public String[] COVARIATES = null; /* - * Use the standard set of covariates in addition to the ones listed using the -cov argument + * The Cycle and Context covariates are standard and are included by default unless this argument is provided. + * Note that the ReadGroup and QualityScore covariates are required and cannot be excluded. */ - @Argument(fullName = "standard_covs", shortName = "standard", doc = "Use the standard set of covariates in addition to the ones listed using the -cov argument", required = false) - public boolean USE_STANDARD_COVARIATES = true; + @Argument(fullName = "no_standard_covs", shortName = "noStandard", doc = "Do not use the standard set of covariates, but rather just the ones listed using the -cov argument", required = false) + public boolean DO_NOT_USE_STANDARD_COVARIATES = false; ///////////////////////////// // Debugging-only Arguments @@ -172,8 +175,8 @@ public class RecalibrationArgumentCollection { argumentsTable.addColumn(RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME); argumentsTable.addRowID("covariate", true); argumentsTable.set("covariate", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, (COVARIATES == null) ? "null" : Utils.join(",", COVARIATES)); - argumentsTable.addRowID("standard_covs", true); - argumentsTable.set("standard_covs", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, USE_STANDARD_COVARIATES); + argumentsTable.addRowID("no_standard_covs", true); + argumentsTable.set("no_standard_covs", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES); argumentsTable.addRowID("run_without_dbsnp", true); argumentsTable.set("run_without_dbsnp", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP); argumentsTable.addRowID("solid_recal_mode", true); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java index c49ff8b47..9c6460320 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java @@ -247,7 +247,7 @@ public class RecalibrationReport { RAC.COVARIATES = value.toString().split(","); else if (argument.equals("standard_covs")) - RAC.USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value); + RAC.DO_NOT_USE_STANDARD_COVARIATES = Boolean.parseBoolean((String) value); else if (argument.equals("solid_recal_mode")) RAC.SOLID_RECAL_MODE = RecalDataManager.SOLID_RECAL_MODE.recalModeFromString((String) value); diff --git a/public/testdata/exampleGRP.grp b/public/testdata/exampleGRP.grp index 619d6b212..2ec55ec57 100644 --- a/public/testdata/exampleGRP.grp +++ b/public/testdata/exampleGRP.grp @@ -11,11 +11,11 @@ insertions_default_quality 45 low_quality_tail 2 mismatches_context_size 2 mismatches_default_quality -1 +no_standard_covs false quantizing_levels 16 run_without_dbsnp false solid_nocall_strategy THROW_EXCEPTION solid_recal_mode SET_Q_ZERO -standard_covs true #:GATKTable:3:94:::; #:GATKTable:Quantized:Quality quantization map