VCF output exception "Can't fetch base outside region"

[pd3]

I've encountered the same problem as described in https://github.com/broadinstitute/pilon/issues/4.

A test case to reproduce the problem can be downloaded from here ftp://ngs.sanger.ac.uk/scratch/project/team145/pd3/pilon-crash.tgz

Briefly, this is the command

 java -Xms8000m -Xmx8000m -jar pilon-1.22.jar --diploid --changes --vcf \
    --chunksize 1000000 --nostrays --genome ref.fa --frags test.bam  \
    --targets 000033F:1000001-1359045 --outdir out/ 2>&1 | tee out.log

and it ends with this exception

Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: java.lang.IllegalArgumentException: requirement failed: can't fetch base outside region at scala.Predef$.require(Predef.scala:224) at org.broadinstitute.pilon.GenomeRegion.refBase(GenomeRegion.scala:735) at org.broadinstitute.pilon.Vcf.writeRecord(Vcf.scala:94) at org.broadinstitute.pilon.GenomeRegion$$anonfun$writeVcf$1.apply$mcVI$sp(GenomeRegion.scala:592) at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160) at org.broadinstitute.pilon.GenomeRegion.writeVcf(GenomeRegion.scala:577) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$5$$anonfun$apply$5.apply(GenomeFile.scala:151) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$5$$anonfun$apply$5.apply(GenomeFile.scala:148) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$5.apply(GenomeFile.scala:148) at org.broadinstitute.pilon.GenomeFile$$anonfun$processRegions$5.apply(GenomeFile.scala:141) at scala.collection.immutable.List.foreach(List.scala:381) at org.broadinstitute.pilon.GenomeFile.processRegions(GenomeFile.scala:141) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:101) at org.broadinstitute.pilon.Pilon.main(Pilon.scala) ... 6 more

[w1bw]

Belated thanks for making this reasonably-sized test case! I'll look into it as soon as I get a chance!

[pd3]

For now I've been running pilon with this temporary fix

diff --git a/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala b/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala
index e1a00e5..05a9d16 100644
--- a/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala
+++ b/src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala
@@ -732,9 +732,13 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)
   }

   def refBase(locus: Int) = {
-    require(inRegion(locus), "can't fetch base outside region")
-    //bases(index(locus)).toChar.toUpper
-    contigBases(locus - 1).toChar.toUpper
+    if ( !inRegion(locus) )
+    {
+        log("Warning: can't fetch base "+locus+", it is outside of the region: "+contig.getName+":"+start+"-"+stop+", replacing with N\n")
+        "N";
+    }
+    else
+        contigBases(locus - 1).toChar.toUpper

[lijingbu]

Same error message. But if remove the "--vcf" option, everything works. You can use other tools to generate vcf.