diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index f8af762e1..e285862d1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -762,7 +762,14 @@ public class VariantEvalWalker extends RodWalker implements Tr } for ( Object o : t.getColumnKeys() ) { - String c = (String) o; + String c; + + if (o instanceof String) { + c = (String) o; + } else { + c = o.toString(); + } + table.addColumn(c, 0.0); } } else { @@ -779,7 +786,12 @@ public class VariantEvalWalker extends RodWalker implements Tr } for (int col = 0; col < t.getColumnKeys().length; col++) { - String c = (String) t.getColumnKeys()[col]; + String c; + if (t.getColumnKeys()[col] instanceof String) { + c = (String) t.getColumnKeys()[col]; + } else { + c = t.getColumnKeys()[col].toString(); + } String newStateKey = stateKey.toString() + r; table.set(newStateKey, c, t.getCell(row, col)); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 840b94a15..285695526 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -17,7 +17,7 @@ import org.broadinstitute.sting.utils.report.utils.TableType; */ @Analysis(name = "Indel length histograms", description = "Shows the distrbution of insertion/deletion event lengths (negative for deletion, positive for insertion)") public class IndelLengthHistogram extends VariantEvaluator { - private static final int SIZE_LIMIT = 50; + private static final int SIZE_LIMIT = 100; @DataPoint(description="Histogram of indel lengths") IndelHistogram indelHistogram = new IndelHistogram(SIZE_LIMIT); @@ -83,21 +83,19 @@ public class IndelLengthHistogram extends VariantEvaluator { } } - public boolean enabled() { return false; } + public boolean enabled() { return true; } public String getName() { return "IndelLengthHistogram"; } public int getComparisonOrder() { return 1; } // need only the evals public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - //System.out.println("Update1 called"); if ( ! vc1.isBiallelic() && vc1.isIndel() ) { //veWalker.getLogger().warn("[IndelLengthHistogram] Non-biallelic indel at "+ref.getLocus()+" ignored."); return vc1.toString(); // biallelic sites are output } if ( vc1.isIndel() ) { - //System.out.println("Is indel"); if ( vc1.isInsertion() ) { indelHistogram.update(vc1.getAlternateAllele(0).length()); } else if ( vc1.isDeletion() ) {