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Fixing a build failure because I want to be completely sure that the code I 

checked in immediately following the build breaking code passes integration
tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5727 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-05-03 02:09:53 +00:00
parent 411980a50a
commit 870e65a685
2 changed files with 2 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -122,7 +122,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*"); private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*"); private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*"); private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
protected static final String EOF_MARKER = "EOF"; public static final String EOF_MARKER = "EOF";
private long numReadsWithMalformedColorSpace = 0; private long numReadsWithMalformedColorSpace = 0;
///////////////////////////// /////////////////////////////

1
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelCountCovariates/IndelCountCovariatesWalker.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
//import org.broadinstitute.sting.gatk.walkers.recalibration.*; //import org.broadinstitute.sting.gatk.walkers.recalibration.*;
//import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer; //import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer;
import org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;