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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-11-14 10:29:09 -05:00
parent e93d461910 ba41f65759
commit 42ddf51156
3 changed files with 6 additions and 4 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
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@ -198,8 +198,6 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
source.close(); source.close();
file.delete(); // this should be last to aid in debugging when the process fails file.delete(); // this should be last to aid in debugging when the process fails
} catch (UserException e) {
throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
} catch (IOException e) { } catch (IOException e) {
throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e); throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
} }

3
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.report; package org.broadinstitute.sting.gatk.report;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
public enum GATKReportVersion { public enum GATKReportVersion {
/** /**
@ -91,6 +92,6 @@ public enum GATKReportVersion {
if (header.startsWith("#:GATKReport.v1.1")) if (header.startsWith("#:GATKReport.v1.1"))
return GATKReportVersion.V1_1; return GATKReportVersion.V1_1;
throw new ReviewedStingException("Unknown GATK report version in header: " + header); throw new UserException.BadInput("The GATK report has an unknown/unsupported version in the header: " + header);
} }
} }

5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -659,7 +659,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
return (g !=null && !g.isHomRef() && (g.isCalled() || (g.isFiltered() && !EXCLUDE_FILTERED))); return (g !=null && !g.isHomRef() && (g.isCalled() || (g.isFiltered() && !EXCLUDE_FILTERED)));
} }
private boolean haveSameGenotypes(Genotype g1, Genotype g2) { private boolean haveSameGenotypes(final Genotype g1, final Genotype g2) {
if ( g1 == null || g2 == null )
return false;
if ((g1.isCalled() && g2.isFiltered()) || if ((g1.isCalled() && g2.isFiltered()) ||
(g2.isCalled() && g1.isFiltered()) || (g2.isCalled() && g1.isFiltered()) ||
(g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED)) (g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))