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Updated recalibrator and cleaner to output full command-lines in the bam header 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3972 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-08 04:39:18 +00:00
parent 0da0dfa1da
commit 3f6e44dc71
2 changed files with 23 additions and 30 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -45,6 +45,7 @@ import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineUtils;
import java.io.File;
import java.io.FileWriter;
@ -224,6 +225,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
programRecord.setProgramVersion(headerInfo.getString("org.broadinstitute.sting.gatk.version"));
HashSet<Object> args = new HashSet<Object>();
args.add(this);
programRecord.setCommandLine(CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), args, getClass()));
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);

49
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -27,11 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.ResourceBundle;
import java.util.*;
import java.util.regex.Pattern;
import net.sf.samtools.*;
@ -46,7 +42,6 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.classloader.PackageUtils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.QualityUtils;
@ -54,11 +49,7 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.ArgumentDefinition;
import org.broadinstitute.sting.commandline.ArgumentSource;
import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
@ -261,27 +252,25 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
programRecord.setProgramVersion( headerInfo.getString("org.broadinstitute.sting.gatk.version") );
String commandLineString = "Covariates=[";
HashSet<Object> args = new HashSet<Object>();
args.add(RAC);
StringBuffer sb = new StringBuffer();
sb.append(CommandLineUtils.createApproximateCommandLineArgumentString(getToolkit(), args, getClass()));
sb.append(" Covariates=[");
for( Covariate cov : requestedCovariates ) {
commandLineString += cov.getClass().getSimpleName() + ", ";
sb.append(cov.getClass().getSimpleName());
sb.append(", ");
}
commandLineString = commandLineString.substring( 0, commandLineString.length() - 2 ); // Trim off the trailing comma
commandLineString += "], ";
// Add all of the arguments from the recalibration argument collection to the command line string
final Field[] fields = RAC.getClass().getFields();
for( Field field : fields ) {
final ArgumentTypeDescriptor atd = ArgumentTypeDescriptor.create(field.getType());
final List<ArgumentDefinition> adList = atd.createArgumentDefinitions(new ArgumentSource(field.getType(), field));
for( ArgumentDefinition ad : adList ) {
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 += "maxQ=" + MAX_QUALITY_SCORE + ", ";
commandLineString += "smoothing=" + SMOOTHING;
programRecord.setCommandLine( commandLineString );
sb.setCharAt(sb.length()-2, ']');
sb.setCharAt(sb.length()-1, ' ');
sb.append("pQ=");
sb.append(PRESERVE_QSCORES_LESS_THAN);
sb.append(" maxQ=");
sb.append(MAX_QUALITY_SCORE);
sb.append(" smoothing=");
sb.append(SMOOTHING);
programRecord.setCommandLine(sb.toString());
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);