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The recalFile argument is no longer added into the PG tag of a bam produced by TableRecalibration. Based on a request from the Sanger. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2625 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-19 15:25:57 +00:00
parent e1fba42fdb
commit a12465b6d5
4 changed files with 9 additions and 12 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -57,7 +57,7 @@ public class RecalDataManager {
private static boolean warnUserNullReadGroup = false; private static boolean warnUserNullReadGroup = false;
private static boolean warnUserNoColorSpace = false; private static boolean warnUserNoColorSpace = false;
public static final String versionString = "v2.2.13"; // Major version, minor version, and build number public static final String versionString = "v2.2.14"; // Major version, minor version, and build number
RecalDataManager() { RecalDataManager() {
data = new NestedHashMap(); data = new NestedHashMap();

12
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -179,7 +179,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// At this point all the covariates should have been found and initialized // At this point all the covariates should have been found and initialized
if( requestedCovariates.size() < 2 ) { if( requestedCovariates.size() < 2 ) {
throw new StingException( "Malformed input recalibration file. Covariate names can't be found in file: " + RAC.RECAL_FILE ); throw new StingException( "Malformed input recalibration csv file. Covariate names can't be found in file: " + RAC.RECAL_FILE );
} }
final boolean createCollapsedTables = true; final boolean createCollapsedTables = true;
@ -226,15 +226,17 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
for( Covariate cov : requestedCovariates ) { for( Covariate cov : requestedCovariates ) {
commandLineString += cov.getClass().getSimpleName() + ", "; commandLineString += cov.getClass().getSimpleName() + ", ";
} }
commandLineString = commandLineString.substring(0, commandLineString.length() - 2); // trim off the trailing comma commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma
commandLineString += "] "; commandLineString += "] ";
// Add all of the arguments from the recalibraiton argument collection to the command line string // Add all of the arguments from the recalibration argument collection to the command line string
final Field[] fields = RAC.getClass().getFields(); final Field[] fields = RAC.getClass().getFields();
for( Field field : fields ) { for( Field field : fields ) {
final ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType()); final ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
final List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field)); final List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
for( ArgumentDefinition ad : adList ) { for( ArgumentDefinition ad : adList ) {
commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", "); if( !ad.fullName.equalsIgnoreCase( "recalFile" ) && !ad.fullName.equalsIgnoreCase( "recal_file" ) ) { // recalFile argument is not added to the PG tag
commandLineString += (ad.fullName + "=" + JVMUtils.getFieldValue(field, RAC) + ", ");
}
} }
} }
commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", "; commandLineString += "pQ = " + PRESERVE_QSCORES_LESS_THAN + ", ";
@ -242,7 +244,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
programRecord.setCommandLine( commandLineString ); programRecord.setCommandLine( commandLineString );
header.addProgramRecord( programRecord ); header.addProgramRecord( programRecord );
// write out the new header // Write out the new header
OUTPUT_BAM.writeHeader( header ); OUTPUT_BAM.writeHeader( header );
} }
} }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnalyzeAnnotationsWalker.java
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@ -3,11 +3,9 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RODRecordList;
import org.broadinstitute.sting.gatk.refdata.RodVCF; import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.io.IOException; import java.io.IOException;

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
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@ -4,10 +4,7 @@ import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.util.HashMap; import java.util.*;
import java.util.TreeSet;
import java.util.Map;
import java.util.Iterator;
import java.io.PrintStream; import java.io.PrintStream;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;