From 458bbdee8fea389ab7e3f554bd7759d37957cc0e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sun, 12 Aug 2012 10:27:05 -0400 Subject: [PATCH] Add useful logger.info telling us the mismatch and indel context sizes --- .../utils/recalibration/covariates/ContextCovariate.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 4c20284d9..13ea0f0b3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; +import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.BaseUtils; @@ -43,6 +44,7 @@ import java.util.ArrayList; */ public class ContextCovariate implements StandardCovariate { + private final static Logger logger = Logger.getLogger(ContextCovariate.class); private int mismatchesContextSize; private int indelsContextSize; @@ -63,6 +65,9 @@ public class ContextCovariate implements StandardCovariate { public void initialize(final RecalibrationArgumentCollection RAC) { mismatchesContextSize = RAC.MISMATCHES_CONTEXT_SIZE; indelsContextSize = RAC.INDELS_CONTEXT_SIZE; + + logger.info("Context sizes: base substitution model " + mismatchesContextSize + ", indel substitution model " + indelsContextSize); + 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)); if (indelsContextSize > MAX_DNA_CONTEXT)