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Moved over to be a walker inside the GATK 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-05-06 18:28:03 +00:00
parent 78409dca0d
commit 0e58fb7cc0
2 changed files with 45 additions and 47 deletions
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81
java/src/org/broadinstitute/sting/utils/tools/LiftoverVCF.java → java/src/org/broadinstitute/sting/gatk/walkers/LiftoverVCF.java
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@ -23,15 +23,18 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.utils.tools; package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.commandline.Argument; 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.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broad.tribble.vcf.VCFRecord; import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFCodec;
import java.io.File; import java.io.File;
import java.util.List;
import net.sf.picard.liftover.LiftOver; import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval; import net.sf.picard.util.Interval;
@ -41,19 +44,8 @@ import net.sf.samtools.SAMFileReader;
/** /**
* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
*/ */
public class LiftoverVCF extends CommandLineProgram { @Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFCodec.class))
public class LiftoverVCF extends RodWalker<Integer, Integer> {
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) @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
protected File CHAIN = null; protected File CHAIN = null;
@ -61,41 +53,56 @@ public class LiftoverVCF extends CommandLineProgram {
@Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true) @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true)
protected File NEW_SEQ_DICT = null; protected File NEW_SEQ_DICT = null;
@Override private VCFWriter writer;
protected int execute() {
VCFReader reader = new VCFReader(VCF); private LiftOver liftOver;
VCFWriter writer = new VCFWriter(OUT);
writer.writeHeader(reader.getHeader());
LiftOver liftOver = new LiftOver(CHAIN); private long successfulIntervals = 0, failedIntervals = 0;
public void initialize() {
liftOver = new LiftOver(CHAIN);
liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH); liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader(); final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary()); liftOver.validateToSequences(toHeader.getSequenceDictionary());
}
long successfulIntervals = 0, failedIntervals = 0; private void convertAndWrite(VCFRecord record) {
while ( reader.hasNext() ) { final Interval fromInterval = new Interval(record.getChr(), record.getStart(), record.getEnd());
VCFRecord record = reader.next(); final Interval toInterval = liftOver.liftOver(fromInterval);
final Interval fromInterval = new Interval(record.getChr(), record.getStart(), record.getEnd()); if ( toInterval != null ) {
final Interval toInterval = liftOver.liftOver(fromInterval); record.setLocation(toInterval.getSequence(), toInterval.getStart());
if ( writer == null ) {
if ( toInterval != null ) { writer = new VCFWriter(out);
record.setLocation(toInterval.getSequence(), toInterval.getStart()); writer.writeHeader(record.getHeader());
writer.addRecord(record);
successfulIntervals++;
} else {
failedIntervals++;
} }
writer.addRecord(record);
successfulIntervals++;
} else {
failedIntervals++;
} }
}
reader.close(); public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
writer.close(); if ( tracker == null )
return 0;
System.out.println("Converted " + successfulIntervals + " intervals; failed to convert " + failedIntervals + " intervals."); List<Object> rods = tracker.getReferenceMetaData("vcf");
for ( Object rod : rods )
convertAndWrite((VCFRecord)rod);
return 0; return 0;
} }
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; }
public void onTraversalDone(Integer result) {
writer.close();
System.out.println("Converted " + successfulIntervals + " intervals; failed to convert " + failedIntervals + " intervals.");
}
} }

9
packages/LiftoverVCF.xml
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@ -1,9 +0,0 @@
<?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>