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Refreshes the mount points that we'll be using (so that the program will play nicely with LSF). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-21 20:36:12 +00:00
parent b5ad5176f7
commit 287bb52e81
1 changed files with 6 additions and 5 deletions
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11
java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
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@ -2,10 +2,7 @@ package org.broadinstitute.sting.secondarybase;
import net.sf.samtools.*; import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram; import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
@ -135,7 +132,11 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
private File getTempSAMFile(String prefix) { private File getTempSAMFile(String prefix) {
try { try {
File tempFile = File.createTempFile(prefix, ".sam", SAM_OUT.getParentFile()); File tempFile = File.createTempFile(prefix, ".sam", SAM_OUT.getParentFile());
tempFile.deleteOnExit(); //tempFile.deleteOnExit();
// Ensure that the volumes we're about to use are ready.
PathUtils.refreshVolume(tempFile);
PathUtils.refreshVolume(new File(System.getProperty("java.io.tmpdir")));
return tempFile; return tempFile;
} catch (IOException e) { } catch (IOException e) {