/*
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:
* 2015 : moving to knime
* 2014 : creation
*/
package com.github.lindenb.jvarkit.tools.misc;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.IOException;
import java.util.Comparator;
import java.util.List;
import htsjdk.samtools.util.BlockCompressedOutputStream;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.SortingCollection;
import htsjdk.tribble.index.Index;
import htsjdk.tribble.index.tabix.TabixFormat;
import htsjdk.tribble.index.tabix.TabixIndexCreator;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.util.TabixUtils;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParametersDelegate;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.bio.bed.BedLine;
import com.github.lindenb.jvarkit.util.bio.bed.BedLineCodec;
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;
@Program(name="bedindextabix",description="Index and sort a Bed on the fly with Tabix.")
public class BedIndexTabix
extends Launcher
{
private static final Logger LOG = Logger.build(BedIndexTabix.class).make();
@Parameter(names={"-o","--output"},description="Output file.",required=true)
private File outputFile = null;
@Parameter(names={"-s","--sort"},description="sort BED prior to saving")
private boolean sort=false;
@ParametersDelegate
private WritingSortingCollection writingSortingCollection = new WritingSortingCollection();
private final BedLineCodec bedCodec=new BedLineCodec();
private static class BedDataCodec extends AbstractDataCodec<String>
{
@Override
public String decode(DataInputStream dis)
throws IOException
{
try {
String s= AbstractDataCodec.readString(dis);
return s;
} catch (Exception e) {
return null;
}
}
@Override
public void encode(DataOutputStream dos, String s) throws IOException {
AbstractDataCodec.writeString(dos, s);
}
@Override
public BedDataCodec clone() {
return new BedDataCodec();
}
};
public BedIndexTabix()
{
}
protected void run(LineIterator in) throws IOException
{
int bedLineCount=0;
File tbi = new File(outputFile.getPath()+TabixUtils.STANDARD_INDEX_EXTENSION);
BlockCompressedOutputStream writer=null;
SortingCollection<String> sorter=null;
final Comparator<String> comparator=new Comparator<String> ()
{
@Override
public int compare(String o1, String o2)
{
BedLine bed1 = bedCodec.decode(o1);
BedLine bed2 = bedCodec.decode(o2);
int i= bed1.getContig().compareTo(bed2.getContig());
if(i!=0) return i;
i= bed1.getStart() - bed2.getStart();
if(i!=0) return i;
i= bed1.getEnd() - bed2.getEnd();
if(i!=0) return i;
return o1.compareTo(o2);
}
};
CloseableIterator<String> iter=null;
try {
TabixIndexCreator indexCreator=new TabixIndexCreator(TabixFormat.BED);
LOG.info("Opening"+outputFile);
writer = new BlockCompressedOutputStream(this.outputFile);
StringBuilder header=new StringBuilder();
while(in.hasNext())
{
String h=in.peek();
if(!BedLine.isBedHeader(h)) break;
header.append(in.next()).append('\n');
}
//write header
if(header.length()>0)
{
LOG.info("Writing header");
writer.write(header.toString().getBytes());
}
if(this.sort)
{
LOG.info("Sorting");
sorter = SortingCollection.newInstance(
String.class,
new BedDataCodec(),
comparator,
this.writingSortingCollection.getMaxRecordsInRam(),
this.writingSortingCollection.getTmpDirectories()
);
while(in.hasNext())
{
String line = in.next();
BedLine bed = bedCodec.decode(line);
if(bed==null) continue;
sorter.add(line);
}
sorter.doneAdding();
sorter.setDestructiveIteration(true);
iter= sorter.iterator();
long filePosition= writer.getFilePointer();
while(iter.hasNext())
{
String line = iter.next();
BedLine bed = this.bedCodec.decode(line);
writer.write(line.getBytes());
writer.write('\n');
indexCreator.addFeature(bed, filePosition);
filePosition = writer.getFilePointer();
}
sorter.cleanup();
}
else
{
long filePosition= writer.getFilePointer();
while(in.hasNext())
{
String line = in.next();
BedLine bed = this.bedCodec.decode(line);
if(bed==null) continue;
writer.write(line.getBytes());
writer.write('\n');
indexCreator.addFeature(bed, filePosition);
filePosition = writer.getFilePointer();
}
}
writer.flush();
LOG.info("Creating index");
Index index = indexCreator.finalizeIndex(writer.getFilePointer());
LOG.info("Writing index to "+tbi+ " using "+index.getClass());
index.writeBasedOnFeatureFile(this.outputFile);
writer.close();
writer=null;
LOG.info("Done N="+bedLineCount);
}
catch (Exception e)
{
if(this.outputFile.exists() &&this.outputFile.isFile())
{
LOG.warning("Deleting "+this.outputFile);
this.outputFile.delete();
if(tbi.exists() && tbi.isFile()) tbi.delete();
}
throw new IOException(e);
}
finally
{
CloserUtil.close(iter);
CloserUtil.close(sorter);
CloserUtil.close(writer);
}
}
@Override
public int doWork(final List<String> args) {
LineIterator r = null;
if(this.outputFile==null)
{
LOG.error(getProgramName()+" output file undefined.");
return -1;
}
if(!this.outputFile.getName().endsWith(".bed.gz"))
{
LOG.error("output file should en with .bed.gz but got "+outputFile);
return -1;
}
try {
if(args.isEmpty())
{
r = IOUtils.openStdinForLineIterator();
}
else if(args.size()==1)
{
r= IOUtils.openURIForLineIterator(args.get(0));
}
else
{
LOG.error("Illegal number of arguments.");
return -1;
}
run(r);
return 0;
} catch (Exception e)
{
LOG.error(e);
return -1;
}
finally
{
CloserUtil.close(r);
}
}
public static void main(String[] args)
{
new BedIndexTabix().instanceMainWithExit(args);
}
}