/*
The MIT License (MIT)
Copyright (c) 2014 Pierre Lindenbaum
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.
History:
* 2014 creation
*/
package com.github.lindenb.jvarkit.tools.sortvcfonref;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.IOException;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.AbstractVCFCodec;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParametersDelegate;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.htsjdk.HtsjdkVersion;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
import com.github.lindenb.jvarkit.util.picard.AbstractDataCodec;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
import com.github.lindenb.jvarkit.util.vcf.VCFUtils;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.SortingCollection;
/**
* Sort a VCF on the INFO field
*
*/
@Program(name="sortvcfoninfo",description="Sort a VCF a field in the INFO column")
public class SortVcfOnInfo extends Launcher
{
private static final Logger LOG = Logger.build(SortVcfOnInfo.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-T","--tag","-t"},description="INFO tag",required=true)
private String infoField=null;
private VCFInfoHeaderLine infoDecl;
private AbstractVCFCodec codec;
@ParametersDelegate
private WritingSortingCollection writingSortingCollection=new WritingSortingCollection();
public SortVcfOnInfo()
{
}
private class VcfLine
implements Comparable<VcfLine>
{
VariantContext ctx=null;
String line;
VcfLine()
{
}
public VcfLine(final String line)
{
this.line=line;
}
public String getObject()
{
Object o=getContext().getAttribute(SortVcfOnInfo.this.infoField);
if(o==null) return null;
if(o.getClass().isArray())
{
Object array[]=(Object[])o;
o = Arrays.asList(array);
}
if(o instanceof List)
{
@SuppressWarnings("rawtypes")
final List L=(List)o;
if(L.isEmpty()) return null;
for(Object o2:L)
{
if(o2==null || o2.equals(".")) continue;
return o2.toString();
}
return null;
}
return o.toString();
}
@Override
public int compareTo(final VcfLine other)
{
final String o1=getObject();
final String o2=other.getObject();
if(o1==null)
{
if(o2==null) return line.compareTo(other.line);
return -1;
}
else if(o2==null)
{
return 1;
}
switch(infoDecl.getType())
{
case Float:
{
return new BigDecimal(o1).compareTo(new BigDecimal(o2));
}
case Integer:
{
return new BigInteger(o1).compareTo(new BigInteger(o2));
}
default:
{
return o1.compareTo(o2);
}
}
}
@Override
public int hashCode() {
return line.hashCode();
}
@Override
public boolean equals(Object obj) {
return line.equals(VcfLine.class.cast(obj).line);
}
@Override
public String toString() {
return line;
}
VariantContext getContext()
{
if(this.ctx==null) this.ctx=SortVcfOnInfo.this.codec.decode(this.line);
return this.ctx;
}
}
private class VariantCodec extends AbstractDataCodec<VcfLine>
{
@Override
public VcfLine decode(DataInputStream dis) throws IOException
{
VcfLine cpl=new VcfLine();
try
{
cpl.line=readString(dis);
}
catch(IOException err)
{
return null;
}
return cpl;
}
@Override
public void encode(DataOutputStream dos, VcfLine s)
throws IOException {
writeString(dos,s.line);
}
@Override
public VariantCodec clone() {
return new VariantCodec();
}
}
private class VariantComparator implements Comparator<VcfLine>
{
@Override
public int compare(VcfLine o1, VcfLine o2)
{
return o1.compareTo(o2);
}
}
@Override
public int doWork(final List<String> args)
{
CloseableIterator<VcfLine> iter=null;
VariantContextWriter w=null;
SortingCollection<VcfLine> sorted=null;
LineIterator r=null;
try {
if(args.isEmpty())
{
LOG.info("reading from stdin");
r=IOUtils.openStreamForLineIterator(stdin());
}
else if(args.size()==1)
{
String filename=args.get(0);
LOG.info("Reading "+filename);
r=IOUtils.openURIForLineIterator(filename);
}
else
{
LOG.error("Illegal number of arguments.");
return -1;
}
final VCFUtils.CodecAndHeader ch=VCFUtils.parseHeader(r);
VCFHeader header=ch.header;
this.codec=ch.codec;
this.infoDecl=header.getInfoHeaderLine(this.infoField);
if(this.infoDecl==null)
{
final StringBuilder msg=new StringBuilder("VCF doesn't contain the INFO field :"+infoField+". Available:");
for(VCFInfoHeaderLine vil:header.getInfoHeaderLines()) msg.append(" ").append(vil.getID());
LOG.error(msg.toString());
return -1;
}
SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(header);
header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"CmdLine",String.valueOf(getProgramCommandLine())));
header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"Version",String.valueOf(getVersion())));
header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"HtsJdkVersion",HtsjdkVersion.getVersion()));
header.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"HtsJdkHome",HtsjdkVersion.getHome()));
w=super.openVariantContextWriter(this.outputFile);
w.writeHeader(header);
sorted=SortingCollection.newInstance(
VcfLine.class,
new VariantCodec(),
new VariantComparator(),
this.writingSortingCollection.getMaxRecordsInRam(),
this.writingSortingCollection.getTmpDirectories()
);
sorted.setDestructiveIteration(true);
while(r.hasNext())
{
final VcfLine vc=new VcfLine(r.next());
progress.watch(vc.getContext());
sorted.add(vc);
}
CloserUtil.close(r);r=null;
sorted.doneAdding();
progress.finish();
iter =sorted.iterator();
while(iter.hasNext())
{
w.add(iter.next().getContext());
}
iter.close();
iter=null;
w.close();
w=null;
return 0;
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
finally
{
CloserUtil.close(r);
CloserUtil.close(iter);
try {
if(sorted!=null) sorted.cleanup();
} catch(Exception err){}
CloserUtil.close(w);
}
}
/**
* @param args
*/
public static void main(String[] args) {
new SortVcfOnInfo().instanceMainWithExit(args);
}
}