unique PG ID used in generated SAM/BAM file headers

Author: Qi Zheng

AlignerBoost/src/edu/upenn/egricelab/AlignerBoost/FilterSAMAlignPE.java

@@ -105,8 +105,8 @@ public static void main(String[] args) {
 
 		SAMFileHeader header = inHeader.clone(); // copy the inFile header as outFile header
 		// Add new programHeader
-		SAMProgramRecord progRec = new SAMProgramRecord(progName);
-		progRec.setProgramName(progName);
+		SAMProgramRecord progRec = new SAMProgramRecord(progName + " run filterPE");
+		progRec.setProgramName(progName + " run filterPE");
 		progRec.setProgramVersion(progVer);
 		progRec.setCommandLine(StringUtils.join(" ", args));
 		header.addProgramRecord(progRec);

AlignerBoost/src/edu/upenn/egricelab/AlignerBoost/FilterSAMAlignSE.java

@@ -102,8 +102,8 @@ public static void main(String[] args) {
 
 		SAMFileHeader header = inHeader.clone(); // copy the inFile header as outFile header
 		// Add new programHeader
-		SAMProgramRecord progRec = new SAMProgramRecord(progName);
-		progRec.setProgramName(progName);
+		SAMProgramRecord progRec = new SAMProgramRecord(progName + " run filterSE");
+		progRec.setProgramName(progName + " run filterSE");
 		progRec.setProgramVersion(progVer);
 		progRec.setCommandLine(StringUtils.join(" ", args));
 		header.addProgramRecord(progRec);

AlignerBoost/src/edu/upenn/egricelab/AlignerBoost/utils/ClassifySAM.java

@@ -63,8 +63,8 @@ public static void main(String[] args) {
 			// clone and modify the header
 			SAMFileHeader header = samIn.getFileHeader().clone(); // copy the inFile header as outFile header
 			// Add new programHeader
-			SAMProgramRecord progRec = new SAMProgramRecord(progName);
-			progRec.setProgramName(progName);
+			SAMProgramRecord progRec = new SAMProgramRecord(progName + " utils classifySAM");
+			progRec.setProgramName(progName + " utils classifySAM");
 			progRec.setProgramVersion(progVer);
 			progRec.setCommandLine(StringUtils.join(" ", args));
 			header.addProgramRecord(progRec);

AlignerBoost/src/edu/upenn/egricelab/AlignerBoost/utils/FilterSamById.java

@@ -56,7 +56,16 @@ public static void main(String[] args) {
 		idFilter = new HashSet<String>();
 		try {
 			samIn = inFactory.open(new File(inFile));
-			samOut = outFactory.makeSAMOrBAMWriter(samIn.getFileHeader().clone(), true, new File(outFile));
+			// clone and modify the header
+			SAMFileHeader header = samIn.getFileHeader().clone(); // copy the inFile header as outFile header
+			// Add new programHeader
+			SAMProgramRecord progRec = new SAMProgramRecord(progName + " utils filterSamById");
+			progRec.setProgramName(progName + " utils filterSamById");
+			progRec.setProgramVersion(progVer);
+			progRec.setCommandLine(StringUtils.join(" ", args));
+			header.addProgramRecord(progRec);
+			
+			samOut = outFactory.makeSAMOrBAMWriter(header, true, new File(outFile));
 			idIn = new BufferedReader(new FileReader(idFile));
 
 			// Read in ID list