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From "Paul King (JIRA)" <j...@apache.org>
Subject [jira] [Closed] (GROOVY-4851) NullPointerException on iterator() call
Date Mon, 12 Jun 2017 00:13:21 GMT

     [ https://issues.apache.org/jira/browse/GROOVY-4851?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Paul King closed GROOVY-4851.
-----------------------------

> NullPointerException on iterator() call
> ---------------------------------------
>
>                 Key: GROOVY-4851
>                 URL: https://issues.apache.org/jira/browse/GROOVY-4851
>             Project: Groovy
>          Issue Type: Bug
>          Components: groovy-runtime
>    Affects Versions: 1.7.10, 1.8-rc-3, 1.8-rc-4, 1.8.0
>         Environment: Linux Mint 10
>            Reporter: Michal
>            Assignee: John Wagenleitner
>             Fix For: 2.5.0-beta-1
>
>         Attachments: ex1.bam, ex1.bam.bai, GROOVY-4851.patch
>
>
> I got with the following code which use http://sourceforge.net/projects/picard/files/picard-tools/
 
> {code}
> 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() 
> } 
> {code}
> I got the following error: 
> {code}
> 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) 
> {code}
> The following code is written completely in Java and uses the same input file without
any error: 
> {code}
> 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);	
>         } 
>         } 
>         } 
> } 
> {code}
> and it produced this output: 
> {code}
> 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 
> ... 
> {code}
> Tim Yates wrote the following work around for this problem:
> {code}
> 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"
>   }
> }
> {code}
> More information can be found here ( http://groovy.329449.n5.nabble.com/NullPointerException-problem-td4360426.html
)



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