SamJavascript.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.

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



import java.io.File;

/**
 * Author: Pierre Lindenbaum PhD. @yokofakun
 * Motivation http://www.biostars.org/p/66319/ 
 */

import java.util.List;

import javax.script.Bindings;
import javax.script.CompiledScript;

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;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;

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

/**
BEGIN_DOC

## Motivation

Filters a BAM using javascript( java rhino engine).
The script puts 'record' a SamRecord (http://picard.sourceforge.net/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html)  
and 'header' ( http://picard.sourceforge.net/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ) in the script context .

END_DOC
*/
@Program(name="samjs",description="Filters a BAM using javascript ( java nashorn engine  ).")
public class SamJavascript
	extends Launcher
	{
	private static final Logger LOG = Logger.build(SamJavascript.class).make();


	@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	private File outputFile = null;


	@Parameter(names={"-X","--fail"},description="Save dicarded reads in that file")
	private File failingReadsFile = null;

	@Parameter(names={"-N","--limit"},description="limit to 'N' records.")
	private long LIMIT = -1L ;

	@ParametersDelegate
	private WritingBamArgs writingBamArgs = new WritingBamArgs();
	
	@Parameter(names={"-e","--expression"},description="javascript expression")
	private String jsExpression=null;
	@Parameter(names={"-f","--file"},description="javascript file")
	private File jsFile =null;
	
	
	private CompiledScript  script=null;
	private SAMFileWriter failingReadsWriter=null;
	

	public SamJavascript()
		{
		
		}
	
	/* open failing bam if it was not already open */
	private void openFailing(final SAMFileHeader h)
		{
		if(this.failingReadsFile==null) return;
		if(this.failingReadsWriter==null)
			{
			LOG.info("Writing failings to "+ this.failingReadsFile);
			final SAMFileHeader h2= h.clone();
			
		
			this.failingReadsWriter=this.writingBamArgs.openSAMFileWriter(failingReadsFile, h2,true);
			}
		}
	
	private void failing(SAMRecord rec,SAMFileHeader h)
		{
		openFailing(h);
		if(failingReadsWriter!=null) failingReadsWriter.addAlignment(rec);
		}
	
	@Override
	public int doWork(List<String> args) {
		SAMRecordIterator iter=null;
		SamReader samFileReader=null;
		SAMFileWriter sw=null;
		try
			{
			this.script  = super.compileJavascript(this.jsExpression,this.jsFile);
			samFileReader= openSamReader(oneFileOrNull(args));
			final SAMFileHeader header=samFileReader.getFileHeader();
			sw = writingBamArgs.openSAMFileWriter(outputFile,header, true);
			
			
			long count=0L;
	        Bindings bindings = this.script.getEngine().createBindings();
	        bindings.put("header", samFileReader.getFileHeader());
	        SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(header);
	        iter = samFileReader.iterator();
			while(iter.hasNext())
				{
				final SAMRecord record=iter.next();
				progress.watch(record);
				bindings.put("record", record);
				
				if(super.evalJavaScriptBoolean(this.script, bindings))
					{
					++count;
					sw.addAlignment(record);
					if(this.LIMIT>0L && count>=this.LIMIT) break;
					
					}
				else
					{
					failing(record,header);
					}
				}
			sw.close();
			/* create empty if never called */
			openFailing(header);
			
			return RETURN_OK;
			}
		catch(final Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(iter);
			CloserUtil.close(samFileReader);
			CloserUtil.close(sw);
			CloserUtil.close(failingReadsWriter);
			}
		}
	
		
	public static void main(String[] args) throws Exception
		{
		new SamJavascript().instanceMainWithExit(args);
		}
	
	

	
	}