/*
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.bamstats04;
import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;
import java.util.Arrays;
import java.util.List;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.util.bio.bed.BedLine;
import com.github.lindenb.jvarkit.util.bio.bed.BedLineCodec;
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;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
/**
BEGIN_DOC
## Example
```
$ java -jar dist/bamstats04.jar \
-B data.bed \
f.bam
#chrom start end length mincov maxcov mean nocoveragebp percentcovered
1 429665 429785 120 42 105 72.36666666666666 0 100
1 430108 430144 36 9 9 9.0 0 100
1 439811 439904 93 0 36 3.6451612903225805 21 77
1 550198 550246 48 1325 1358 1344.4583333333333 0 100
1 629855 629906 51 223 520 420.70588235294116 0 100
1 689960 690029 69 926 1413 1248.9420289855072 0 100
1 690852 690972 120 126 193 171.24166666666667 0 100
1 787283 787406 123 212 489 333.9756097560976 0 100
1 789740 789877 137 245 688 528.6715328467153 0 1
```
END_DOC
*/
@Program(name="bamstats04",
description="Coverage statistics for a BED file.",
keywords={"bam","coverage","statistics","bed"}
)
public class BamStats04 extends Launcher
{
private static final Logger LOG = Logger.build(BamStats04.class).make();
@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
private File outputFile = null;
@Parameter(names={"-cov","--cov"},description="min coverage to say the position is not covered")
private int MIN_COVERAGE = 0 ;
@Parameter(names={"-mmq","--mmq"},description="min mapping quality")
private int MMQ = 0 ;
@Parameter(names={"-keeporphan","--keeporphan"},description="if set: accept not properly aligned pairs.")
private boolean keep_orphans = false;
@Parameter(names={"-B","--bed"},description="Bed File. Required",required=true)
private File bedFile = null;
@Parameter(names={"-R","--ref"},description="Optional REFerence Genome. If set, a column with the GC% will be added")
private File faidxFile = null;
@Override
public int doWork(final List<String> args) {
if(this.bedFile==null || !this.bedFile.exists()) {
LOG.error("undefined option -B");
return -1;
}
BufferedReader bedIn=null;
SamReader samReader = null;
PrintWriter pw = null;
IndexedFastaSequenceFile indexedFastaSequenceFile=null;
GenomicSequence genomicSequence=null;
try
{
final BedLineCodec codec= new BedLineCodec();
bedIn=IOUtils.openFileForBufferedReading(this.bedFile);
samReader = super.openSamReader(oneFileOrNull(args));
if(this.faidxFile!=null) {
indexedFastaSequenceFile = new IndexedFastaSequenceFile(this.faidxFile);
}
pw = super.openFileOrStdoutAsPrintWriter(this.outputFile);
pw.println("#chrom\tstart\tend\tlength\t"+
(indexedFastaSequenceFile==null?"":"gc_percent\t")+
"mincov\tmaxcov\tmeancov\tmediancov\tnocoveragebp\tpercentcovered");
String line=null;
while((line=bedIn.readLine())!=null)
{
if(line.isEmpty() || line.startsWith("#")) continue;
final BedLine bedLine = codec.decode(line);
if(bedLine==null) continue;
if(indexedFastaSequenceFile!=null && (genomicSequence==null || !genomicSequence.getChrom().equals(bedLine.getContig()))) {
genomicSequence = new GenomicSequence(indexedFastaSequenceFile, bedLine.getContig());
}
/* picard javadoc: - Sequence name - Start position (1-based) - End position (1-based, end inclusive) */
final int counts[]=new int[bedLine.getEnd()-bedLine.getStart()+1];
if(counts.length==0) continue;
Arrays.fill(counts, 0);
/**
* start - 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.
* end - 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.
*/
final SAMRecordIterator r=samReader.queryOverlapping(
bedLine.getContig(),
bedLine.getStart(),
bedLine.getEnd()
);
while(r.hasNext())
{
final SAMRecord rec=r.next();
if(rec.getReadUnmappedFlag()) continue;
if(rec.getReadFailsVendorQualityCheckFlag()) continue;
if(rec.getDuplicateReadFlag() ) continue;
if(!this.keep_orphans && rec.getReadPairedFlag() && !rec.getProperPairFlag())
{
continue;
}
if(rec.isSecondaryOrSupplementary()) continue;
if(!rec.getReferenceName().equals(bedLine.getContig())) continue;
if(rec.getMappingQuality()==255 ||
rec.getMappingQuality()==0 ||
rec.getMappingQuality()< this.MMQ)
{
continue;
}
final Cigar cigar=rec.getCigar();
if(cigar==null) continue;
int refpos1=rec.getAlignmentStart();
for(final CigarElement ce:cigar)
{
final CigarOperator op=ce.getOperator();
if(!op.consumesReferenceBases()) continue;
if(op.consumesReadBases())
{
for(int i=0;i< ce.getLength();++i)
{
if(refpos1+i>= bedLine.getStart() && refpos1+i<=bedLine.getEnd())
{
counts[refpos1+i-bedLine.getStart()]++;
}
}
}
refpos1+=ce.getLength();
if(refpos1>bedLine.getEnd()) break;
}
}
r.close();
Arrays.sort(counts);
int count_no_coverage=0;
double mean=0;
for(final int cov:counts)
{
if(cov<=MIN_COVERAGE) ++count_no_coverage;
mean+=cov;
}
mean/=counts.length;
final double median_depth;
final int mid_x= counts.length/2;
if(counts.length%2==0)
{
median_depth = (counts[mid_x-1]+counts[mid_x])/2.0;
}
else
{
median_depth = counts[mid_x];
}
pw.println(
bedLine.getContig()+"\t"+
(bedLine.getStart()-1)+"\t"+
(bedLine.getEnd())+"\t"+
counts.length+"\t"+
(genomicSequence==null?
"":
String.valueOf((genomicSequence.getGCPercent(bedLine.getStart()-1,bedLine.getEnd())).getGCPercentAsInteger())+"\t")+
counts[0]+"\t"+
counts[counts.length-1]+"\t"+
mean+"\t"+median_depth+"\t"+
count_no_coverage+"\t"+
(int)(((counts.length-count_no_coverage)/(double)counts.length)*100.0)
);
}
pw.flush();
pw.close();pw=null;
LOG.info("done");
return RETURN_OK;
}
catch(final Exception err)
{
LOG.error(err);
return -1;
}
finally
{
CloserUtil.close(indexedFastaSequenceFile);
CloserUtil.close(pw);
CloserUtil.close(bedIn);
CloserUtil.close(samReader);
}
}
/**
* @param args
*/
public static void main(String[] args) throws Exception
{
new BamStats04().instanceMain(args);
}
}