https://www.biostars.org/p/368754/ jvarkit java bed bam

README.md

usage:

$ ls input.bed
$ java -jar dist/samjdk.jar --body -f biostar368754.code input.bam

biostar368754.code

private IntervalTreeMap<Interval> treemap = null;
@Override
public Object apply(final SAMRecord record) {
  
	/** first time, fill the interval map */
	if(this.treemap==null) {
		try	{
			/** first call , read the bed */
			this.treemap = new IntervalTreeMap<>();
			/** read all the lines */
			IOUtil.slurpLines(new java.io.File("input.bed")).
				stream().
				filter(L->!L.isEmpty()). /* remove empty lines */
				map(L->L.split("[\t]")). /* split tab */
				map(T->new Interval(T[0],1+Integer.parseInt(T[1]),Integer.parseInt(T[2]))). /* convert to Interval */
				forEach(I->treemap.put(I,I));/* fill the treemap */
			} catch(java.io.IOException err) {
		throw new RuntimeIOException(err);
		}
	}
if(!record.getReadUnmappedFlag()) {
   /** the read interval */
   final Interval readInterval = new Interval(record.getContig(),record.getStart(),record.getEnd());
   if(treemap.containsOverlapping(readInterval) ) return false;
}

/* mate interval */
if(record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
	final int mateEnd= SAMUtils.getMateCigar(record)!=null?
			SAMUtils.getMateAlignmentEnd(record):
			record.getMateAlignmentStart()
			;

	final Interval mateInterval = new Interval(record.getMateReferenceName(),record.getMateAlignmentStart(),mateEnd);
        if(treemap.containsOverlapping(mateInterval) ) return false;
	}
return true;
}