From 81313d9452185213e01a983eb4fd40683bf9e379 Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Feb 2010 14:41:50 +0000
Subject: [PATCH] added class VCFMerge

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2840 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/tools/vcf/VCFMerge.java  | 116 ++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java

diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java
new file mode 100644
index 000000000..dee796b0d
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java
@@ -0,0 +1,116 @@
+package org.broadinstitute.sting.playground.tools.vcf;
+import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+import org.broadinstitute.sting.utils.genotype.vcf.*;
+
+import edu.mit.broad.picard.util.Interval;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+
+
+import java.io.*;
+import java.util.*;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileWalker;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
+
+//import org.apache.commons.math.optimization.*;
+//import org.apache.commons.math.optimization.direct.*;
+//import org.apache.commons.math.analysis.MultivariateRealFunction;
+
+// Program for frequency-specific  VCF-files.
+
+
+/**
+ * @author jmaguire
+ */
+
+
+class VCFMerge extends CommandLineProgram 
+{
+
+		@Argument(fullName = "vcf1", shortName = "vcf1", doc = "file to open", required = true) public String filename1;
+		@Argument(fullName = "vcf2", shortName = "vcf2", doc = "file to open", required = true) public String filename2;
+		@Argument(fullName = "out", shortName = "out", doc = "file to write results to", required = true) public String output_filename;
+		@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
+		@Argument(fullName = "verbose", shortName = "verbose", doc = "print way too much debugging output", required = false) public Boolean verbose = false;
+
+		@Override
+		protected int execute() 
+		{
+			VCFReader reader1;
+			VCFReader reader2;
+
+			if (autocorrect) 
+			{ 
+				reader1 = new VCFReader(VCFHomogenizer.create(filename1)); 
+				reader2 = new VCFReader(VCFHomogenizer.create(filename2)); 
+			}
+			else 
+			{ 
+				reader1 = new VCFReader(new File(filename1)); 
+				reader2 = new VCFReader(new File(filename2)); 
+			}
+		
+			VCFHeader header1 = reader1.getHeader();
+			VCFHeader header2 = reader2.getHeader();
+
+			VCFRecord record1 = reader1.next();
+			VCFRecord record2 = reader2.next();
+
+			VCFWriter writer = new VCFWriter(new File(output_filename));
+			writer.writeHeader(header1);
+
+			while(true)
+			{
+				if ((record1 == null) && (record2 == null)) { break; }
+				else if (record1 == null) { writer.addRecord(record2); record2 = reader2.next(); continue; }
+				else if (record2 == null) { writer.addRecord(record1); record1 = reader1.next(); continue; }
+
+				if (verbose)
+				{
+					System.out.printf("RECORD1: %s\n", record1.toStringEncoding(header1));
+					System.out.printf("RECORD2: %s\n", record2.toStringEncoding(header2));
+				}
+
+				if (record1.isFiltered()) { record1 = reader1.next(); continue; }
+				if (record2.isFiltered()) { record2 = reader2.next(); continue; }
+
+				Interval interval1 = VCFTool.getIntervalFromRecord(record1);
+				Interval interval2 = VCFTool.getIntervalFromRecord(record2);
+
+				int comparison = VCFTool.compareIntervals(interval1, interval2);
+				
+				if (comparison == 0)
+				{
+					// records match! Emit one.
+					writer.addRecord(record1);
+					record1 = reader1.next();
+					record2 = reader2.next();
+				}
+				else if (comparison > 0)
+				{
+					writer.addRecord(record2);
+					record2 = reader2.next();
+				}
+				else if (comparison < 0)
+				{
+					writer.addRecord(record1);
+					record1 = reader1.next();
+				}
+			}
+
+			writer.close();
+
+			return 0;
+		}
+}
+
+