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You can have an error so early that some engine fields are uninitialized. Commit protects RunReport from these errors 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4185 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-09-01 19:00:25 +00:00
parent a975db2c2e
commit 995cfe34fe
2 changed files with 7 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -976,7 +976,7 @@ public class GenomeAnalysisEngine {
* @return cumulative metrics about the entire run. * @return cumulative metrics about the entire run.
*/ */
public ReadMetrics getCumulativeMetrics() { public ReadMetrics getCumulativeMetrics() {
return readsDataSource.getCumulativeReadMetrics(); return readsDataSource == null ? null : readsDataSource.getCumulativeReadMetrics();
} }
/** /**

8
java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -182,8 +182,6 @@ public class GATKRunReport {
Date end = new java.util.Date(); Date end = new java.util.Date();
endTime = dateFormat.format(end); endTime = dateFormat.format(end);
runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds
nIterations = engine.getCumulativeMetrics().getNumIterations();
nReads = engine.getCumulativeMetrics().getNumReadsSeen();
tmpDir = System.getProperty("java.io.tmpdir"); tmpDir = System.getProperty("java.io.tmpdir");
// deal with memory usage // deal with memory usage
@ -191,6 +189,12 @@ public class GATKRunReport {
maxMemory = Runtime.getRuntime().maxMemory(); maxMemory = Runtime.getRuntime().maxMemory();
totalMemory = Runtime.getRuntime().totalMemory(); totalMemory = Runtime.getRuntime().totalMemory();
// we can only do some operations if an error hasn't occurred
if ( engine.getCumulativeMetrics() != null ) {
// it's possible we aborted so early that these data structures arent initialized
nIterations = engine.getCumulativeMetrics().getNumIterations();
nReads = engine.getCumulativeMetrics().getNumReadsSeen();
}
// user and hostname -- information about the runner of the GATK // user and hostname -- information about the runner of the GATK
userName = System.getProperty("user.name"); userName = System.getProperty("user.name");