/*
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.samfixcigar;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
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;
import com.github.lindenb.jvarkit.util.picard.GenomicSequence;
/**
BEGIN_DOC
### Example
the input file
```
$ cat toy.sam
@SQ SN:ref LN:45
@SQ SN:ref2 LN:40
r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA *
r003 0 ref 9 30 5H6M * 0 0 AGCTAA *
r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC *
r003 16 ref 29 30 6H5M * 0 0 TAGGC *
r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
x1 0 ref2 1 30 20M * 0 0 aggttttataaaacaaataa ????????????????????
x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ?????????????????????
x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ??????????????????????????
x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ?????????????????????????
x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ????????????????????????
x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ???????????????????????
```
processing with samfixcigar
```
$ java -jar dist/samfixcigar.jar \
-r samtools-0.1.19/examples/toy.fa \
samtools-0.1.19/examples/toy.sam
@HD VN:1.4 SO:unsorted
@SQ SN:ref LN:45
@SQ SN:ref2 LN:40
r001 163 ref 7 30 8=4I4=1D3= = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
r002 0 ref 9 30 1S2I6=1P1I1P1I1X1=2X2I * 0 0 AAAAGATAAGGGATAAA *
r003 0 ref 9 30 2=1X3= * 0 0 AGCTAA *
r004 0 ref 16 30 6=14N1I5= * 0 0 ATAGCTCTCAGC *
r003 16 ref 29 30 5= * 0 0 TAGGC *
r001 83 ref 37 30 9= = 7 -39 CAGCGCCAT *
x1 0 ref2 1 30 16=1X3= * 0 0 AGGTTTTATAAAACAAATAA ????????????????????
x2 0 ref2 2 30 15=1X3=1X1= * 0 0 GGTTTTATAAAACAAATAATT ?????????????????????
x3 0 ref2 6 30 9=4I13= * 0 0 TTATAAAACAAATAATTAAGTCTACA ??????????????????????????
x4 0 ref2 10 30 1X3=1X20= * 0 0 CAAATAATTAAGTCTACAGAGCAAC ?????????????????????????
x5 0 ref2 12 30 2=1X21= * 0 0 AATAATTAAGTCTACAGAGCAACT ????????????????????????
x6 0 ref2 14 30 1X22= * 0 0 TAATTAAGTCTACAGAGCAACTA ???????????????????????
```
### Usage in the literature
This tool was cited in Extensive sequencing of seven human genomes to characterize benchmark reference materials Sci Data. 2016; 3: 160025..
*/
@Program(name="samfixcigar",description="Fix Cigar String in SAM replacing 'M' by 'X' or '='")
public class SamFixCigar extends Launcher
{
private static final Logger LOG = Logger.build(SamFixCigar.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-r","-R","--reference"},description=INDEXED_FASTA_REFERENCE_DESCRIPTION,required=true)
private File faidx = null;
@ParametersDelegate
private WritingBamArgs writingBamArgs=new WritingBamArgs();
private IndexedFastaSequenceFile indexedFastaSequenceFile=null;
@Override
public int doWork(List<String> args) {
if(this.faidx==null)
{
LOG.error("Reference was not specified.");
return -1;
}
GenomicSequence genomicSequence=null;
SamReader sfr=null;
SAMFileWriter sfw=null;
try
{
this.indexedFastaSequenceFile=new IndexedFastaSequenceFile(faidx);
sfr = openSamReader(oneFileOrNull(args));
final SAMFileHeader header=sfr.getFileHeader();
sfw = this.writingBamArgs.
setReferenceFile(this.faidx).
openSAMFileWriter(outputFile,header, true);
final SAMSequenceDictionaryProgress progress= new SAMSequenceDictionaryProgress(header);
final List<CigarElement> newCigar=new ArrayList<CigarElement>();
final SAMRecordIterator iter=sfr.iterator();
while(iter.hasNext())
{
final SAMRecord rec=progress.watch(iter.next());
Cigar cigar=rec.getCigar();
byte bases[]=rec.getReadBases();
if( rec.getReadUnmappedFlag() ||
cigar==null ||
cigar.getCigarElements().isEmpty() ||
bases==null)
{
sfw.addAlignment(rec);
continue;
}
if(genomicSequence==null ||
genomicSequence.getSAMSequenceRecord().getSequenceIndex()!=rec.getReferenceIndex())
{
genomicSequence=new GenomicSequence(indexedFastaSequenceFile, rec.getReferenceName());
}
newCigar.clear();
int refPos1=rec.getAlignmentStart();
int readPos0=0;
for(final CigarElement ce:cigar.getCigarElements())
{
final CigarOperator op = ce.getOperator();
if(op.equals(CigarOperator.M))
{
for(int i=0;i< ce.getLength();++i)
{
char c1=Character.toUpperCase((char)bases[readPos0]);
char c2=Character.toUpperCase(refPos1-1< genomicSequence.length()?genomicSequence.charAt(refPos1-1):'*');
if(c2=='N' || c1==c2)
{
newCigar.add(new CigarElement(1, CigarOperator.EQ));
}
else
{
newCigar.add(new CigarElement(1, CigarOperator.X));
}
refPos1++;
readPos0++;
}
}
else
{
newCigar.add(ce);
if(op.consumesReadBases()) readPos0+=ce.getLength();
if(op.consumesReferenceBases()) refPos1+=ce.getLength();
}
}
int i=0;
while(i< newCigar.size())
{
final CigarOperator op1 = newCigar.get(i).getOperator();
final int length1 = newCigar.get(i).getLength();
if( i+1 < newCigar.size() &&
newCigar.get(i+1).getOperator()==op1)
{
final CigarOperator op2= newCigar.get(i+1).getOperator();
int length2=newCigar.get(i+1).getLength();
newCigar.set(i,new CigarElement(length1+length2, op2));
newCigar.remove(i+1);
}
else
{
++i;
}
}
cigar=new Cigar(newCigar);
//info("changed "+rec.getCigarString()+" to "+newCigarStr+" "+rec.getReadName()+" "+rec.getReadString());
rec.setCigar(cigar);
sfw.addAlignment(rec);
}
progress.finish();
return RETURN_OK;
}
catch(Exception err)
{
LOG.error(err);
return -1;
}
finally
{
CloserUtil.close(this.indexedFastaSequenceFile);
CloserUtil.close(sfr);
CloserUtil.close(sfw);
}
}
/**
* @param args
*/
public static void main(String[] args) {
new SamFixCigar().instanceMainWithExit(args);
}
}