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Even more conservative limit on number of differences to summarize at 1000

This commit is contained in:
Mark DePristo 2012-05-26 14:44:37 -04:00
parent 31f4e5b52e
commit 86e5a066fc
2 changed files with 6 additions and 4 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
View File

@ -225,10 +225,10 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
public void onTraversalDone(Integer sum) {
//out.printf("Reading master file %s%n", masterFile);
DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
out.printf(" Read %d objects%n", master.size());
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);
out.printf(" Read %d objects%n", test.size());
logger.info(String.format("Read %d objects", test.size()));
// out.printf("Master diff objects%n");
// out.println(master.toString());
@ -236,7 +236,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
// out.println(test.toString());
List<Difference> diffs = diffEngine.diff(master, test);
out.printf(" Done computing diff, n = %d%n", diffs.size());
logger.info(String.format("Done computing diff with %d differences found", diffs.size()));
if ( showItemizedDifferences ) {
out.printf("Itemized results%n");
for ( Difference diff : diffs )
@ -246,5 +246,6 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff, maxRawDiffsToSummary);
params.setDescending(false);
diffEngine.reportSummarizedDifferences(diffs, params);
logger.info(String.format("Done summarizing differences"));
}
}

3
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -48,6 +48,7 @@ public class MD5DB {
* Subdirectory under the ant build directory where we store integration test md5 results
*/
private static final int MAX_RECORDS_TO_READ = 10000;
private static final int MAX_RAW_DIFFS_TO_SUMMARIZE = 1000;
public static final String LOCAL_MD5_DB_DIR = "integrationtests";
public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
@ -250,7 +251,7 @@ public class MD5DB {
// TODO -- capture output and put in log
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(baos);
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0, MAX_RECORDS_TO_READ);
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0, MAX_RAW_DIFFS_TO_SUMMARIZE);
boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
if ( success ) {
final String content = baos.toString();