groovy

NullPointerException on iterator() call

Details

  • Type: Bug Bug
  • Status: Open Open
  • Priority: Major Major
  • Resolution: Unresolved
  • Affects Version/s: 1.7.10, 1.8-rc-3, 1.8-rc-4, 1.8.0
  • Fix Version/s: 2.1.x
  • Component/s: None
  • Labels:
    None
  • Environment:
    Linux Mint 10
  • Number of attachments :
    2

Description

I got with the following code which use http://sourceforge.net/projects/picard/files/picard-tools/ 

import net.sf.picard.util.Interval 
import net.sf.picard.util.IntervalList 
import net.sf.picard.util.SamLocusIterator 
import net.sf.picard.util.SamLocusIterator.RecordAndOffset 
import net.sf.samtools.SAMFileHeader 
import net.sf.samtools.SAMFileReader 
import net.sf.samtools.SAMFileReader.ValidationStringency 

bamFile = new File("/media/trx/workspace/Picard/test/ex1.bam") 
baiFile = new File(bamFile.getAbsolutePath() + ".bai") 

sam = new SAMFileReader(bamFile, baiFile, true) 

sam.setValidationStringency(ValidationStringency.SILENT) 
if(!sam.hasIndex()) throw new Exception("Missing index") 

SAMFileHeader header = sam.getFileHeader() 

sequences = header.getSequenceDictionary().getSequences() 

for ( i in sequences) { 
        println("${i.getSequenceName()} = ${i.getSequenceLength()}") 
} 

IntervalList il = new IntervalList(header) 
il.add(new Interval("chr1",0, 157)) 
final SamLocusIterator sli = new SamLocusIterator(sam, il, true) 
sli.setEmitUncoveredLoci(false) 

sli.each { li -> 
        println li.getSequenceName() 
}

I got the following error: 

chr1 = 1575 
chr2 = 1584 
WARNING	2011-04-30 12:10:29	SamLocusIterator	SamLocusIterator constructed with samReader that has SortOrder == unsorted.  Assuming SAM is coordinate sorted, but exceptions may occur if it is not. 
Exception in thread "main" java.lang.NullPointerException 
        at net.sf.picard.util.SamLocusIterator.samHasMore(SamLocusIterator.java:223) 
        at net.sf.picard.util.SamLocusIterator.hasNext(SamLocusIterator.java:231) 
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1219) 
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:1196) 
        at org.codehaus.groovy.runtime.dgm$110.invoke(Unknown Source) 
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:270) 
        at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:52) 
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:40) 
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116) 
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:124) 
        at pileup.run(pileup.groovy:33) 
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) 
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
        at java.lang.reflect.Method.invoke(Method.java:616) 
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90) 
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233) 
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1058) 
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:886) 
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:793) 
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:776) 
        at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:394) 
        at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source) 
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:40) 
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116) 
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128) 
        at pileup.main(pileup.groovy)

The following code is written completely in Java and uses the same input file without any error: 

import java.io.File; 
import java.util.List; 
import net.sf.picard.util.Interval; 
import net.sf.picard.util.IntervalList; 
import net.sf.picard.util.SamLocusIterator; 
import net.sf.picard.util.SamLocusIterator.LocusInfo; 
import net.sf.picard.util.SamLocusIterator.RecordAndOffset; 
import net.sf.samtools.SAMFileHeader; 
import net.sf.samtools.SAMFileReader; 
import net.sf.samtools.SAMRecord; 
import net.sf.samtools.SAMRecordIterator; 
import net.sf.samtools.SAMSequenceRecord; 
import net.sf.samtools.SAMFileReader.ValidationStringency; 


public class ReadReferenceName { 

        /** 
         * @param args 
         * @throws Exception 
         */ 
        public static void main(String[] args) throws Exception { 
                // TODO Auto-generated method stub 
                
                File bamFile = new File("/media/trx/workspace/Picard/test/ex1.bam"); 
                File baiFile = new File(bamFile.getAbsolutePath() + ".bai");	
                
                SAMFileReader sam = new SAMFileReader(bamFile, baiFile, true); 
        sam.setValidationStringency(ValidationStringency.SILENT); 
                if(!sam.hasIndex()) throw new Exception("Missing index"); 
                
                SAMFileHeader header = sam.getFileHeader(); 
                List<SAMSequenceRecord> sequences = header.getSequenceDictionary().getSequences(); 
                
                for(SAMSequenceRecord rec: sequences) { 
                        System.out.println(rec.getSequenceName() + " = " + 
                                        rec.getSequenceLength()); 
                } 
                
                IntervalList il = new IntervalList(header); 
                il.add(new Interval("chr1",0, 157)); 
        final SamLocusIterator sli = new SamLocusIterator(sam, il, true); 
        sli.setEmitUncoveredLoci(false); 
      
        for (final SamLocusIterator.LocusInfo li : sli) { 
        String sequenceName = li.getSequenceName(); 
        int pos = li.getPosition(); 
        int coverage = li.getRecordAndPositions().size(); 
        System.out.println(sequenceName + " coverage at base " + pos + " = " 
        + coverage); 
        for (int i = 0; i< coverage; i++){ 
        RecordAndOffset rec = li.getRecordAndPositions().get(i); 
        char base = (char)rec.getReadBase(); 
        String readName = rec.getRecord().getReadName(); 
        System.out.println("  base in read " + readName + " = " + base);	
        } 
        } 
        } 
}

and it produced this output: 

chr1 = 1575 
chr2 = 1584 
WARNING	2011-04-30 19:30:07	SamLocusIterator	SamLocusIterator constructed with samReader that has SortOrder == unsorted.  Assuming SAM is coordinate sorted, but exceptions may occur if it is not. 
chr1 coverage at base 100 = 1 
  base in read EAS56_57:6:190:289:82 = A 
chr1 coverage at base 101 = 1 
...

Tim Yates wrote the following work around for this problem:

import net.sf.picard.util.*
import net.sf.picard.util.SamLocusIterator.RecordAndOffset
import net.sf.samtools.*
import net.sf.samtools.SAMFileReader.ValidationStringency
import net.sf.picard.filter.*
import net.sf.samtools.util.CloseableIterator

bamFile = new File("ex1.bam")
baiFile = new File("ex1.bam.bai")

sam = new SAMFileReader(bamFile, baiFile, true)
sam.validationStringency = ValidationStringency.SILENT
if(!sam.hasIndex()) throw new Exception("Missing index")

SAMFileHeader header = sam.fileHeader
sequences = header.sequenceDictionary.sequences

sequences.each { i ->
  println "$i.sequenceName = $i.sequenceLength"
}

SamLocusIterator.metaClass.iterator = {
  if ( delegate.@samIterator != null ) {
    throw new IllegalStateException("Cannot call iterator() more than once on SamLocusIterator");
  }
  CloseableIterator<SAMRecord> tempIterator;
  if (delegate.@intervals != null) {
    tempIterator = new SamRecordIntervalIteratorFactory().makeSamRecordIntervalIterator(delegate.@samReader, delegate.@intervals, delegate.@useIndex);
  } else {
    tempIterator = delegate.@samReader.iterator();
  }
  if (delegate.@samFilters != null) {
    tempIterator = new FilteringIterator(tempIterator, new AggregateFilter(delegate.@samFilters));
  }
  delegate.@samIterator = new PeekableIterator<SAMRecord>( tempIterator )
  delegate 
}

IntervalList il = new IntervalList( header )
il.add( new Interval( "chr1", 0, 157 ) )
SamLocusIterator sli = new SamLocusIterator( sam, il, true )
sli.emitUncoveredLoci = false

sli.each { li ->
  println "$li.sequenceName coverage at base $li.position = ${li.recordAndPositions.size()}"
  (0..<li.recordAndPositions.size()).each { i ->
    rec = li.recordAndPositions.get( i )
	println "  base in read $rec.record.readName = $rec.readBase"
  }
}

More information can be found here ( http://groovy.329449.n5.nabble.com/NullPointerException-problem-td4360426.html )

  1. File
    ex1.bam
    28/May/11 7:39 PM
    122 kB
    Michal
  2. File
    ex1.bam.bai
    28/May/11 7:39 PM
    0.2 kB
    Michal

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Cedric Champeau added a comment -

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Cedric Champeau added a comment - Formatting tags
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blackdrag blackdrag added a comment -

After further investigation I found this minimal example to reproduce the problem:

class X implements Iterable, Iterator {
    Iterator iterator() {null}
    boolean hasNext(){true}
    def next(){}
    void remove(){}
}


def x = new X()
assert x.iterator() == null

the call to iterator() will not call the declared method, instead it will call the our Iterator#iterator method in DGM. If you remove the Iterator interface it works just fine, so it is only reproducable with both interfaces present

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blackdrag blackdrag added a comment - After further investigation I found this minimal example to reproduce the problem: class X implements Iterable, Iterator { Iterator iterator() { null } boolean hasNext(){ true } def next(){} void remove(){} } def x = new X() assert x.iterator() == null the call to iterator() will not call the declared method, instead it will call the our Iterator#iterator method in DGM. If you remove the Iterator interface it works just fine, so it is only reproducable with both interfaces present
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blackdrag blackdrag added a comment -

reducing the level of this bug, since it is not a common problem and depends on the special occasion of an Itarable being also an Iterator

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blackdrag blackdrag added a comment - reducing the level of this bug, since it is not a common problem and depends on the special occasion of an Itarable being also an Iterator
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blackdrag blackdrag added a comment -

it must be something in generating the method list for this class, that makes things go wrong. DGM has the ability to shadow methods of the class, but here it is from an interface and the class implementation should take precedence

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blackdrag blackdrag added a comment - it must be something in generating the method list for this class, that makes things go wrong. DGM has the ability to shadow methods of the class, but here it is from an interface and the class implementation should take precedence
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Paul King added a comment -

tagging for review for 2.1.0-rc-1 otherwise we should reassign fix version

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Paul King added a comment - tagging for review for 2.1.0-rc-1 otherwise we should reassign fix version

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  • Assignee:
    Unassigned
    Reporter:
    Michal
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  • Created:
    Updated: