[GROOVY-4851] NullPointerException on iterator() call

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 1.7.10, 1.8-rc-3, 1.8-rc-4, 1.8.0
• Fix Version/s: 2.5.0-beta-1
• Component/s: groovy-runtime
• Environment: Linux Mint 10
• Flags: Patch
• Assignee: John Wagenleitner
• Reporter: Michal
• Created: 28/May/11 19:39
• Updated: 12/Jun/17 00:12
• Resolved: 17/May/17 15:39

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 = [e-mail]();
  }
  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 )

Issue Links

• is related to: GROOVY-7937 CLONE - same linkedlist code different behavior between groovy and java (fix priority of DGM methods vs actual methods on an object)