Biostar84452.java

/*
The MIT License (MIT)

Copyright (c) 2015 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 creation

*/
package com.github.lindenb.jvarkit.tools.biostar;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.util.ArrayList;
import java.util.List;


import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.util.CloserUtil;

import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParametersDelegate;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;

/**
BEGIN_DOC

## Example

```bash
$  java -jar dist/biostar84452.jar samtools-0.1.18/examples/toy.sam > out.sam

@HD	VN:1.4	SO:unsorted
@SQ	SN:ref	LN:45
@SQ	SN:ref2	LN:40
@PG	ID:0	PN:com.github.lindenb.jvarkit.tools.biostar.Biostar84452	VN:b5ebf67dd2926d8a6afadb4d1e36a4959508057f	CL:samtools-0.1.18/examples/toy.sam
(...)
r002	0	ref	9	0	2I6M1P1I1P1I4M2I	*	0	0	AAAGATAAGGGATAAA	*
(...)


$ grep r002 samtools-0.1.18/examples/toy.sam
r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*

```
END_DOC


 */
@Program(name="biostar84452",
	biostars=84452,
	description="remove clipped bases from BAM",
	keywords={"sam","bam","clip"}
	)
public class Biostar84452 extends Launcher
	{
	private static final Logger LOG = Logger.build(Biostar84452.class).make();
	
	
	@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	private File outputFile = null;
	
	@ParametersDelegate
	private WritingBamArgs WritingBamArgs=new WritingBamArgs();
	@Parameter(names={"-t","--tag"},description="tag to flag samrecord as processed")
	private String customTag=null;
	
	@Override
	public int doWork(List<String> args) {
		if(customTag!=null)
			{
			if(customTag.length()!=2 || !customTag.startsWith("X"))
				{
				LOG.error("Bad tag: expect length=2 && start with 'X'");
				return -1;
				}
			}
		SAMFileWriter sfw=null;
		SamReader sfr=null;
		try
			{
			sfr = super.openSamReader(oneFileOrNull(args));
			SAMFileHeader header=sfr.getFileHeader();

			sfw = this.WritingBamArgs.openSAMFileWriter(outputFile, header, true);
			
			
			long nChanged=0L;
			SAMRecordIterator iter=sfr.iterator();
			while(iter.hasNext())
				{
				SAMRecord rec=iter.next();
				if(rec.getReadUnmappedFlag())
					{
					sfw.addAlignment(rec);
					continue;
					}
				
				Cigar cigar=rec.getCigar();
				if(cigar==null)
					{
					sfw.addAlignment(rec);
					continue;
					}
				final String originalCigarSting = rec.getCigarString();
				byte bases[]= rec.getReadBases();
				if(bases==null)
					{
					sfw.addAlignment(rec);
					continue;
					}
				
				ArrayList<CigarElement> L=new ArrayList<CigarElement>();
				ByteArrayOutputStream nseq=new ByteArrayOutputStream();
				ByteArrayOutputStream nqual=new ByteArrayOutputStream();
				
				byte quals[]= rec.getBaseQualities();
				int indexBases=0;
				for(CigarElement ce:cigar.getCigarElements())
					{
					switch(ce.getOperator())
						{
						case S: indexBases+=ce.getLength(); break;
						case H://cont
						case P: //cont
						case N: //cont
						case D:
							{
							L.add(ce);
							break;
							}
							
						case I:
						case EQ:
						case X:
						case M:
							{
							L.add(ce);
							nseq.write(bases,indexBases,ce.getLength());
							if(quals.length!=0) nqual.write(quals,indexBases,ce.getLength());
							indexBases+=ce.getLength(); 
							break;
							}
						default:
							{
							throw new RuntimeException("Unsupported Cigar opertator:"+ce.getOperator());
							}
						}
					
					}
				if(indexBases!=bases.length)
					{
					throw new RuntimeException("ERRROR "+rec.getCigarString());
					}
				if(L.size()==cigar.numCigarElements())
					{
					sfw.addAlignment(rec);
					continue;
					}
				++nChanged;
				if(this.customTag!=null) rec.setAttribute(this.customTag,originalCigarSting);
				rec.setCigar(new Cigar(L));
				rec.setReadBases(nseq.toByteArray());
				if(quals.length!=0)  rec.setBaseQualities(nqual.toByteArray());
				sfw.addAlignment(rec);
				}
			LOG.info("Num records changed:"+nChanged);
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(sfw);
			CloserUtil.close(sfr);
			}
		return 0;
		}
	/**
	 * @param args
	 */
	public static void main(String[] args)
		{
		new Biostar84452().instanceMainWithExit(args);
		}

	}