/*
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.samgrep;
import java.io.BufferedReader;
import java.io.File;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
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;
/**
BEGIN_DOC
### Examples
#### Example 1
```
java -jar dist/samgrep.jar -R r001 -- samtools-0.1.18/examples/toy.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.samgrep.SamGrep VN:dac03b80e9fd88a15648b22550e57d10c9bed725 CL:-R r001 samtools-0.1.18/examples/toy.sam
r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
```
#### Example 4
```
java -jar dist/samgrep.jar -R r001 -- -n 1 samtools-0.1.18/examples/toy.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.samgrep.SamGrep VN:dac03b80e9fd88a15648b22550e57d10c9bed725 CL:-R r001 -n 1 samtools-0.1.18/examples/toy.sam
r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
```
END_DOC
*/
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
### Examples
#### Example 1
```
java -jar dist/samgrep.jar -R r001 -- samtools-0.1.18/examples/toy.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.samgrep.SamGrep VN:dac03b80e9fd88a15648b22550e57d10c9bed725 CL:-R r001 samtools-0.1.18/examples/toy.sam
r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
```
#### Example 4
```
java -jar dist/samgrep.jar -R r001 -- -n 1 samtools-0.1.18/examples/toy.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.samgrep.SamGrep VN:dac03b80e9fd88a15648b22550e57d10c9bed725 CL:-R r001 -n 1 samtools-0.1.18/examples/toy.sam
r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
```
END_DOC
*/
@Program(name="samgrep",description="grep read-names in a bam file")
public class SamGrep extends Launcher
{
private static final Logger LOG = Logger.build(SamGrep.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-R","--readname"},description="add the read name")
private Set<String> nameStrings = new HashSet<>();
@Parameter(names={"-f","--readfile"},description="file containing a list of read names")
private File namefile = null;
@Parameter(names={"-x","--tee"},description="if output fileame specified, continue to output original input to stdout.")
private boolean divertToStdout = false;
@Parameter(names={"-n","--stopafter"},description="when found, remove the read from the list of names when found more that 'n' time (increase speed)")
private int n_before_remove = -1 ;
@Parameter(names={"-V","--invert"},description="invert")
private boolean inverse = false;
@ParametersDelegate
private WritingBamArgs writingBamArgs=new WritingBamArgs();
private final Map<String,Integer> readNames=new HashMap<String,Integer>();
@Override
public int doWork(List<String> args) {
readNames.clear();
if(namefile!=null) {
BufferedReader in=null;
try
{
in=IOUtils.openFileForBufferedReading(this.namefile);
String line;
while((line=in.readLine())!=null)
{
line=line.trim();
if(line.isEmpty()) continue;
readNames.put(line,0);
}
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
finally
{
CloserUtil.close(in);
}
}
for(final String line: this.nameStrings) {
readNames.put(line,0);
}
if(readNames.isEmpty())
{
LOG.warn("no read found.");
}
SAMFileWriter sfw=null;
SAMFileWriter samStdout=null;
SamReader sfr=null;
try {
sfr = super.openSamReader(oneFileOrNull(args));
final SAMFileHeader header=sfr.getFileHeader().clone();
final SAMSequenceDictionaryProgress progress= new SAMSequenceDictionaryProgress(header);
if(this.outputFile==null)
{
sfw = this.writingBamArgs.openSAMFileWriter(null, header, true);
}
else
{
samStdout= this.writingBamArgs.openSAMFileWriter(null, header, true);
sfw= this.writingBamArgs.openSAMFileWriter(outputFile, header, true);
}
SAMRecordIterator iter=sfr.iterator();
while(iter.hasNext())
{
boolean keep=false;
final SAMRecord rec=progress.watch(iter.next());
if(samStdout!=null) samStdout.addAlignment(rec);
Integer count = readNames.get(rec.getReadName());
if(count!=null)
{
keep=true;
}
if(this.inverse) keep=!keep;
if(keep)
{
sfw.addAlignment(rec);
}
if(n_before_remove!=-1 && !inverse && keep)
{
count++;
if(count>=n_before_remove)
{
readNames.remove(rec.getReadName());
if(samStdout==null && readNames.isEmpty()) break;
}
else
{
readNames.put(rec.getReadName(),count);
}
}
}
progress.finish();
return RETURN_OK;
} catch (final Exception err) {
LOG.error(err);
return -1;
} finally {
CloserUtil.close(samStdout);
CloserUtil.close(sfw);
CloserUtil.close(sfr);
}
}
public static void main(final String[] argv)
{
new SamGrep().instanceMainWithExit(argv);
}
}