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More informative error message in AnalyzeCovariates and cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2511 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-06 14:56:29 +00:00
parent bca3d1b943
commit 1c90e6a954
1 changed files with 14 additions and 27 deletions
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41
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -232,52 +232,39 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
// for each read group
for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) {
if(NUM_READ_GROUPS_TO_PROCESS == -1 || ++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS) {
Process p = null;
if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) {
String readGroup = readGroupKey.toString();
System.out.println("Analyzing read group: " + readGroup);
Process p = null;
// for each covariate
for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
Covariate cov = requestedCovariates.get(iii);
try {
if( iii == 1 ) {
// Analyze reported quality
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
IGNORE_QSCORES_LESS_THAN); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
if(numReadGroups % 3 == 0) { // Don't want to spawn all the RScript jobs too quickly. So wait for this one to finish
p.waitFor();
}
} else { // Analyze all other covariates
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
}
} catch (IOException ex) {
try {
Thread.sleep(1600); // wait for 1.6 seconds and then try to spawn the process again
if( iii == 1 ) {
// Analyze reported quality
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
IGNORE_QSCORES_LESS_THAN); // The third argument is the Q scores that should be turned pink in the plot because they were ignored
} else { // Analyze all other covariates
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
}
} catch (InterruptedException e) {
e.printStackTrace();
System.exit(-1);
} catch (IOException e) {
e.printStackTrace();
System.exit(-1);
}
} catch (InterruptedException e) {
e.printStackTrace();
System.exit(-1);
} catch (IOException e) {
System.out.println("Fatal Exception: Perhaps RScript jobs are being spawned too quickly? One work around is to process fewer read groups using the -numRG option.");
e.printStackTrace();
System.exit(-1);
}
}
} else {
} else { // at the maximum number of read groups so break out
break;
}
}