First pass at liftover tool. Passing buck over to Aaron...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/tools/LiftoverVCF.java

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+/*
+ * Copyright (c) 2010.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.tools;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
+import org.broad.tribble.vcf.VCFRecord;
+import org.broad.tribble.vcf.VCFHeader;
+
+import java.util.TreeSet;
+import java.util.HashMap;
+import java.io.File;
+
+import net.sf.picard.liftover.LiftOver;
+import net.sf.picard.util.Interval;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+
+/**
+ * Lifts a VCF file over from one build to another.
+ */
+public class LiftoverVCF extends CommandLineProgram {
+
+    public static void main(String args[]) {
+        LiftoverVCF LO = new LiftoverVCF();
+        CommandLineProgram.start( LO, args );
+        System.exit(0);
+    }
+
+    @Argument(fullName="vcf", shortName="vcf", doc="VCF file to lift over", required=true)
+    protected File VCF = null;
+
+    @Argument(fullName="out", shortName="out", doc="Output VCF file", required=true)
+    protected File OUT = null;
+
+    @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
+    protected File CHAIN = null;
+
+    @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
+    protected File NEW_SEQ_DICT = null;
+
+    @Override
+    protected int execute() {
+
+        VCFReader reader = new VCFReader(VCF);
+        VCFHeader header = reader.getHeader();
+
+        LiftOver liftOver = new LiftOver(CHAIN);
+        liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
+
+        final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
+        liftOver.validateToSequences(toHeader.getSequenceDictionary());
+
+        TreeSet<Interval> sortedIntervals = new TreeSet<Interval>();
+        HashMap<Interval, VCFRecord> intervalsToRecords = new HashMap<Interval, VCFRecord>();
+        long successfulIntervals = 0, failedIntervals = 0;
+
+        while ( reader.hasNext() ) {
+            VCFRecord record = reader.next();
+
+            final Interval fromInterval = new Interval(record.getChr(), record.getStart(), record.getEnd());
+            final Interval toInterval = liftOver.liftOver(fromInterval);
+
+            if ( toInterval != null ) {
+                record.setLocation(toInterval.getSequence(), toInterval.getStart());
+                sortedIntervals.add(toInterval);
+                intervalsToRecords.put(toInterval, record);
+                successfulIntervals++;
+            } else {
+                failedIntervals++;
+            }
+        }
+
+        reader.close();
+
+        System.out.println("Converted " + successfulIntervals + " intervals; failed to convert " + failedIntervals + " intervals.");
+        System.out.println("Writing new VCF...");
+
+        VCFWriter writer = new VCFWriter(OUT);
+        writer.writeHeader(header);
+
+        for ( Interval interval : sortedIntervals )
+            writer.addRecord(intervalsToRecords.get(interval));
+
+        writer.close();
+
+        return 0;
+    }
+}

packages/LiftoverVCF.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<package name="LiftoverVCF">
+  <executable name="LiftoverVCF">
+    <main-class name="org.broadinstitute.sting.utils.tools.LiftoverVCF" />
+    <resource-bundle file="StingText.properties" />
+    <dependencies>
+    </dependencies>
+  </executable>
+</package>