From 86e5a066fcafaa9dbef5a05146f2e8915d189a15 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Sat, 26 May 2012 14:44:37 -0400 Subject: [PATCH] Even more conservative limit on number of differences to summarize at 1000 --- .../sting/gatk/walkers/diffengine/DiffObjectsWalker.java | 7 ++++--- public/java/test/org/broadinstitute/sting/MD5DB.java | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java index 21de6135f..1524a6a7b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java @@ -225,10 +225,10 @@ public class DiffObjectsWalker extends RodWalker { 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 { // out.println(test.toString()); List 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 { 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")); } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java index 6b62cb3cd..52680a078 100644 --- a/public/java/test/org/broadinstitute/sting/MD5DB.java +++ b/public/java/test/org/broadinstitute/sting/MD5DB.java @@ -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();