diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java index 2bf75b035..73301c511 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java @@ -24,6 +24,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; import net.sf.samtools.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -300,7 +301,7 @@ public class GATKBAMIndex { fileChannel = fileStream.getChannel(); } catch (IOException exc) { - throw new ReviewedStingException("Unable to open index file " + mFile, exc); + throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 79362ff2f..5f20ac7af 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; import java.util.Collection;