zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Testing utility to perform diffs N times

This commit is contained in:
Mark DePristo 2012-06-11 12:03:57 -04:00
parent 8014178f2f
commit 6272612808
1 changed files with 47 additions and 36 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
View File

@ -125,7 +125,7 @@ import java.util.List;
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000598.AC 1
</pre>
</pre>
*
* @author Mark DePristo
* @since 7/4/11
@ -201,6 +201,9 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="showItemizedDifferences", shortName="SID", doc="Should we enumerate all differences between the files?", required=false)
boolean showItemizedDifferences = false;
@Argument(fullName="iterations", doc="Number of iterations to perform, should be 1 unless you are doing memory testing", required=false)
int iterations = 1;
DiffEngine diffEngine;
@Override
@ -225,6 +228,13 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
@Override
public void onTraversalDone(Integer sum) {
if ( iterations > 1 ) {
for ( int i = 0; i < iterations; i++ ) {
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, 20, 10, 0, -1, false);
boolean success = DiffEngine.simpleDiffFiles(masterFile, testFile, MAX_OBJECTS_TO_READ, params);
logger.info("Iteration " + i + " success " + success);
}
} else {
//out.printf("Reading master file %s%n", masterFile);
DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
logger.info(String.format("Read %d objects", master.size()));
@ -252,4 +262,5 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
diffEngine.reportSummarizedDifferences(diffs, params);
logger.info(String.format("Done summarizing differences"));
}
}
}