TViewCmd.java

/*
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.tview;

import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;

import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParametersDelegate;
import com.github.lindenb.jvarkit.io.IOUtils;
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 htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.Interval;
/*
BEGIN_DOC

## Example

```
$ java -jar dist/tview.jar -R toy.fa toy.bam --clip  --groupby sample  --insert  --plain

ref:1-61
          POS: 1.......^^..11..^^^^....^^..21........31...^.....41........51
          REF: AGCATGTT**AGATAA****GATA**GCTGTGCTAGTAGGCAG*TCAGCGCCATNNNNNNN
               
ndefined_sample      TT**AGATAAAGAGGATA**-CTG               cagcgccat       
                      AAAAGATAAGG**GATAAA    NNNNNNtaggc                    
                  NNNNN**AGCTAA                                             
                                    ATA**GCT--------------CTCAGC            
ample CONSENSUS      TTAAAGNTAANGAGGATAAAGCTG      TAGGC  CTCAGCGCCAT
efined_sample 3          ********  ****   **                ****     
                         ********  ****   **                ****     
                         ********  ****   **                ****     
                     ************************      *****  ***********
                     ************************      *****  ***********
                     ************************      *****  ***********
               ******************************************************
               ******************************************************
               ******************************************************
             0 ******************************************************
```
            
END_DOC
 */
@Program(name="tview",description="equivalent of samtools tview",keywords={"sam","bam","visualization","terminal"})
public class TViewCmd extends Launcher
	{
	private static final Logger LOG = Logger.build(TViewCmd.class).make();
	@Parameter(names={"-o","--out"},description="Output file . Default: stdout")
	private File outputFile = null;
	@Parameter(names={"-r","--region"},description="Interval list")
	private Set<String> intervalStr = new HashSet<>();
	@Parameter(names={"-width","--width"},description="default screen width")
	private int defaultScreenWidth=-1;
	@Parameter(names={"--nodefaultinterval"},description="if no interval was provided, don't try to create a default one.")
	private boolean nodefaultinterval=false;

	
	@ParametersDelegate
	TView tview = new TView();

	private  Interval parseInterval(final String regionStr) {
		int cols = defaultScreenWidth;
		final String COLUMNS=System.getenv("COLUMNS");
		if(COLUMNS!=null && COLUMNS.matches("[0-9]+")) {
			cols = Integer.parseInt(COLUMNS);
			LOG.info(cols);
			}
		if(cols<=1) cols=60;
		
		final int colon=regionStr.indexOf(':');
		
		int chromStart;
		int chromEnd;

		if(colon==-1)
			{
			return new Interval(regionStr,1,1+cols,false,regionStr);
			}
		final String chrom=regionStr.substring(0,colon);
			
		final int hyphen=regionStr.indexOf('-', colon+1);
		final int plus=regionStr.indexOf('+', colon+1);

		if(plus!=-1 && hyphen!=-1) 
			{
			throw new IllegalArgumentException("colon/plus both in "+regionStr);
			}
		else if(hyphen==-1 && plus==-1)
			{
			chromStart=Integer.parseInt(regionStr.substring(colon+1));
			chromEnd = chromStart + cols;
			}
		else
			{
			if(plus!=-1)
				{
				int pivot = Integer.parseInt(regionStr.substring(colon+1,plus));
				int dx = Integer.parseInt(regionStr.substring(plus+1));
				chromStart=Math.max(1,pivot-dx);
				chromEnd=pivot+dx;
				}
			else
				{
				chromStart= Integer.parseInt(regionStr.substring(colon+1,hyphen));
				chromEnd= Integer.parseInt(regionStr.substring(hyphen+1));
				}
			}
		if(chromStart<0 || chromEnd<chromStart)
			{
			throw new IllegalArgumentException("bad position in "+regionStr);
			}
		return new Interval(chrom, chromStart, chromEnd,false,regionStr);
		}
	
	@Override
	public int doWork(List<String> args) {
		PrintStream out = null;
		try
			{	
			args = new ArrayList<>(IOUtils.unrollFiles(args));
			if(args.isEmpty())
				{
				LOG.error("no BAM file defined");
				return -1;
				}
			final List<SamInputResource> samInputResources= args.stream().map(S->SamInputResource.of(S)).
					collect(Collectors.toList());
			tview.setBamFiles(samInputResources);
			if(tview.initialize()!=0)
				{
				LOG.error("cannot initialize tview");
				return -1;
				}
			final List<Interval> intervals= this.intervalStr.stream().map(S->parseInterval(S) ).collect(Collectors.toList());
			if(!nodefaultinterval && intervals.isEmpty() && !args.isEmpty())
				{
				final SamReader samReader = super.createSamReaderFactory().open(SamInputResource.of(args.get(0)));
					final SAMSequenceDictionary dict=  samReader.getFileHeader()!=null && 
							samReader.getFileHeader().getSequenceDictionary()!=null ? 
							samReader.getFileHeader().getSequenceDictionary() : null
							;
					samReader.close();
				if( dict != null && !dict.isEmpty()) {
					intervals.add(parseInterval(dict.getSequence(0).getSequenceName()));
					}
				}
			
			out = super.openFileOrStdoutAsPrintStream(outputFile);
			
			
			for(final Interval interval : intervals) {
				tview.setInterval(interval);
				tview.paint(out);
			}
			
			out.flush();
			return 0;
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(out);
			CloserUtil.close(tview);
			}
		
		}
	
	public static void main(String[] args)
		{
		new TViewCmd().instanceMainWithExit(args);
		}
	}