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Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.

This commit is contained in:
Eric Banks 2012-07-04 00:21:21 -04:00
parent 7d30558e6f
commit 33306d2e20
4 changed files with 14 additions and 11 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java
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@ -170,7 +170,7 @@ public class RecalDataManager {
final ArrayList<Covariate> requiredCovariates = addRequiredCovariatesToList(requiredClasses); // add the required covariates
ArrayList<Covariate> optionalCovariates = new ArrayList<Covariate>();
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);

17
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -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);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java
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@ -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);

2
public/testdata/exampleGRP.grp vendored
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@ -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