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Add useful logger.info telling us the mismatch and indel context sizes

This commit is contained in:
Mark DePristo 2012-08-12 10:27:05 -04:00
parent 6fefdaf428
commit 458bbdee8f
1 changed files with 5 additions and 0 deletions
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5
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.utils.recalibration.covariates; package org.broadinstitute.sting.utils.recalibration.covariates;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
@ -43,6 +44,7 @@ import java.util.ArrayList;
*/ */
public class ContextCovariate implements StandardCovariate { public class ContextCovariate implements StandardCovariate {
private final static Logger logger = Logger.getLogger(ContextCovariate.class);
private int mismatchesContextSize; private int mismatchesContextSize;
private int indelsContextSize; private int indelsContextSize;
@ -63,6 +65,9 @@ public class ContextCovariate implements StandardCovariate {
public void initialize(final RecalibrationArgumentCollection RAC) { public void initialize(final RecalibrationArgumentCollection RAC) {
mismatchesContextSize = RAC.MISMATCHES_CONTEXT_SIZE; mismatchesContextSize = RAC.MISMATCHES_CONTEXT_SIZE;
indelsContextSize = RAC.INDELS_CONTEXT_SIZE; indelsContextSize = RAC.INDELS_CONTEXT_SIZE;
logger.info("Context sizes: base substitution model " + mismatchesContextSize + ", indel substitution model " + indelsContextSize);
if (mismatchesContextSize > MAX_DNA_CONTEXT) if (mismatchesContextSize > MAX_DNA_CONTEXT)
throw new UserException.BadArgumentValue("mismatches_context_size", String.format("context size cannot be bigger than %d, but was %d", MAX_DNA_CONTEXT, mismatchesContextSize)); throw new UserException.BadArgumentValue("mismatches_context_size", String.format("context size cannot be bigger than %d, but was %d", MAX_DNA_CONTEXT, mismatchesContextSize));
if (indelsContextSize > MAX_DNA_CONTEXT) if (indelsContextSize > MAX_DNA_CONTEXT)