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Added @PG tag to ReduceReads 

Pulled out the functionality from Indel Realigner and Table Recalibrator into Utils.setupWriter to make everyone else's life's easier if they want to include the PG tag in their walkers.
This commit is contained in:
Mauricio Carneiro 2012-03-16 14:09:07 -04:00
parent e4cbeddf2d
commit ec4a870a0f
1 changed files with 35 additions and 0 deletions
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35
public/java/src/org/broadinstitute/sting/utils/Utils.java
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@ -25,9 +25,14 @@
package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMProgramRecord;
import net.sf.samtools.util.StringUtil;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.net.InetAddress;
import java.util.*;
@ -668,4 +673,34 @@ public class Utils {
array[i] = value;
}
public static void setupWriter(StingSAMFileWriter writer, GenomeAnalysisEngine toolkit, boolean preSorted, boolean KEEP_ALL_PG_RECORDS, Object walker, String PROGRAM_RECORD_NAME) {
final SAMProgramRecord programRecord = createProgramRecord(toolkit, walker, PROGRAM_RECORD_NAME);
SAMFileHeader header = toolkit.getSAMFileHeader();
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
for ( SAMProgramRecord record : oldRecords )
if ( !record.getId().startsWith(PROGRAM_RECORD_NAME) || KEEP_ALL_PG_RECORDS )
newRecords.add(record);
newRecords.add(programRecord);
header.setProgramRecords(newRecords);
writer.writeHeader(header);
writer.setPresorted(preSorted);
}
public static SAMProgramRecord createProgramRecord(GenomeAnalysisEngine toolkit, Object walker, String PROGRAM_RECORD_NAME) {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
final ResourceBundle headerInfo = TextFormattingUtils.loadResourceBundle("StingText");
try {
final String version = headerInfo.getString("org.broadinstitute.sting.gatk.version");
programRecord.setProgramVersion(version);
} catch (MissingResourceException e) {
// couldn't care less if the resource is missing...
}
programRecord.setCommandLine(toolkit.createApproximateCommandLineArgumentString(toolkit, walker));
return programRecord;
}
}