Off topic:Using Picard To Get The Depth At A Given Position:

Question

[Pierre Lindenbaum]

(cross-posted on samtools-dev )

I want to get the coverage-depth at a given position : (chr1-12450) using picard:SamLocusIterator

I can clearly see my reads overlapping that position using samtools tview.

 12441     12451     12461     12471     12481     12491     12501              
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
CCAGTGGATTGGCCTAGGTGGGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
ccagtggattggcctaggtgggatctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
CCAGTGGA tggcctaggtgggatctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
ccagtgga   GCCTAGGTGGGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
CCAGTGGAT    CTAGGAGGGATCTCTGAGCTCAACAAGCCCTCTATGGGGGGGAGGTGCAGAGACGGGAGGGGCAGAG
CCAGTGGATTG   taggtgggatctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
CCAGTGGATTGGCCTAG tgggatctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
CCAGTGGATTGGCCTAGG   gatctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
CCAGTGGATTGGCCTAGGTG  atctctgagctcaacaagccctctctgggtggtaggtgcagagacgggaggggcagag
CCAGTGGATTGGCCTAGGTGG     CTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
ccagtggattggcctaggtgggatctct AGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
CCAGTGGATTGGCCTAGGTGGGATCTCTG  ctcaacaaggcctctctgggtggtaggtgcagagacgggaggggcagag

However, using the following program:

 import net.sf.picard.reference.*;
    import net.sf.picard.util.*;
    import net.sf.samtools.*;
    import java.io.*;
    import java.util.*;

    public class Test
        {
        public static void main(String args[])
            {
            SAMFileReader samReader=new SAMFileReader(new File(args[0]));
            String chromId="chr1";
            int chromStart=12450;
            int chromEnd=chromStart;
            Interval interval=new Interval(chromId,chromStart,chromEnd);
            IntervalList iL=new IntervalList(samReader.getFileHeader());
            iL.add(interval);

            SamLocusIterator sli=new SamLocusIterator(samReader,iL,true);


            for(Iterator<SamLocusIterator.LocusInfo>  iter=sli.iterator();
                    iter.hasNext();
                    )
                {
                SamLocusIterator.LocusInfo locusInfo=iter.next();
                System.out.println(
                    "POS="+locusInfo.getPosition()+
                    " depth:"+locusInfo.getRecordAndPositions().size()
                    );
                }
            sli.close();
            samReader.close();
            }
        }

compile and run:

javac -cp /sam-1.77.jar:picard-1.77.jar:. Test.java
java -cp /sam-1.77.jar:picard-1.77.jar:. Test my.bam

produces the following output (depth==0)

POS=12450 depth:0

What's wrong with my program ?

Another problem, my program also raises an exception when sli.close() is invoked:

Exception in thread "main" java.lang.NullPointerException
        at net.sf.picard.util.SamRecordIntervalIterator.close(SamRecordIntervalIterator.java:162)
       (...)
        at net.sf.picard.util.SamLocusIterator.close(SamLocusIterator.java:219)
        at Test.main(Test.java:32)

why ?