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Committing Michael Yourshaw's patch for AnalyzeCovariates. We spawn each RScript process and wait for it to finish in series. Thanks Michael! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4095 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-24 13:06:25 +00:00
parent 9fb151f417
commit 7a8b6b87da
1 changed files with 4 additions and 5 deletions
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9
java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
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@ -265,7 +265,7 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
// for each read group // for each read group
for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) { for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) {
Process p = null; Process p;
if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) { if(++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS || NUM_READ_GROUPS_TO_PROCESS == -1) {
String readGroup = readGroupKey.toString(); String readGroup = readGroupKey.toString();
@ -280,13 +280,12 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " + p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_QualityScoreCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " + OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " +
IGNORE_QSCORES_LESS_THAN + " " + MAX_QUALITY_SCORE + " " + MAX_HISTOGRAM_VALUE); // The third argument is the Q scores that should be turned pink in the plot because they were ignored IGNORE_QSCORES_LESS_THAN + " " + MAX_QUALITY_SCORE + " " + MAX_HISTOGRAM_VALUE); // 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();
p.waitFor();
}
} else { // Analyze all other covariates } else { // Analyze all other covariates
Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " + p = Runtime.getRuntime().exec(PATH_TO_RSCRIPT + " " + PATH_TO_RESOURCES + "plot_residualError_OtherCovariate.R" + " " +
OUTPUT_DIR + readGroup + "." + cov.getClass().getSimpleName()+ ".dat" + " " + 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 cov.getClass().getSimpleName().split("Covariate")[0]); // The third argument is the name of the covariate in order to make the plots look nice
p.waitFor();
} }
} catch (InterruptedException e) { } catch (InterruptedException e) {
e.printStackTrace(); e.printStackTrace();