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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
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83
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
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@ -111,21 +111,21 @@ import java.util.List;
* <p>
*
* <pre>
[testng] path count
[testng] *.*.*.AC 6
[testng] *.*.*.AF 6
[testng] *.*.*.AN 6
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000598.AC 1
</pre>
[testng] path count
[testng] *.*.*.AC 6
[testng] *.*.*.AF 6
[testng] *.*.*.AN 6
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000000.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000117.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AC 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AF 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000211.AN 1
[testng] 64b991fd3850f83614518f7d71f0532f.integrationtest.20:10000598.AC 1
</pre>
*
* @author Mark DePristo
* @since 7/4/11
@ -201,11 +201,14 @@ 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
public void initialize() {
this.diffEngine = new DiffEngine();
this.diffEngine = new DiffEngine();
}
@Override
@ -225,31 +228,39 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
@Override
public void onTraversalDone(Integer sum) {
//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()));
//out.printf("Reading test file %s%n", testFile);
DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
logger.info(String.format("Read %d objects", test.size()));
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()));
//out.printf("Reading test file %s%n", testFile);
DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
logger.info(String.format("Read %d objects", test.size()));
// out.printf("Master diff objects%n");
// out.println(master.toString());
// out.printf("Test diff objects%n");
// out.println(test.toString());
List<Difference> diffs = diffEngine.diff(master, test);
logger.info(String.format("Done computing diff with %d differences found", diffs.size()));
if ( showItemizedDifferences ) {
out.printf("Itemized results%n");
for ( Difference diff : diffs )
out.printf("DIFF: %s%n", diff.toString());
}
List<Difference> diffs = diffEngine.diff(master, test);
logger.info(String.format("Done computing diff with %d differences found", diffs.size()));
if ( showItemizedDifferences ) {
out.printf("Itemized results%n");
for ( Difference diff : diffs )
out.printf("DIFF: %s%n", diff.toString());
}
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out,
MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff,
maxRawDiffsToSummary, doPairwise);
params.setDescending(false);
diffEngine.reportSummarizedDifferences(diffs, params);
logger.info(String.format("Done summarizing differences"));
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out,
MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff,
maxRawDiffsToSummary, doPairwise);
params.setDescending(false);
diffEngine.reportSummarizedDifferences(diffs, params);
logger.info(String.format("Done summarizing differences"));
}
}
}
}