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Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).

This commit is contained in:
Eric Banks 2012-07-18 12:57:34 -04:00
parent f2fe59a9d4
commit ae08d35138
2 changed files with 2 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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@ -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);
}
}

1
public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -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;