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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-07-25 15:10:35 -04:00
parent a29554e565 3afcb3415d
commit a53aeb75ab
3 changed files with 7 additions and 4 deletions
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2
build.xml
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@ -520,6 +520,8 @@
<fileset dir="${java.classes}"> <fileset dir="${java.classes}">
<include name="**/utils/codecs/**/*.class"/> <include name="**/utils/codecs/**/*.class"/>
<include name="**/utils/variantcontext/**/*.class"/> <include name="**/utils/variantcontext/**/*.class"/>
<include name="**/UserException*.class"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset> </fileset>
</jar> </jar>
</target> </target>

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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@ -342,12 +342,12 @@ public class DiffEngine {
return reader.readFromFile(file, maxElementsToRead); return reader.readFromFile(file, maxElementsToRead);
} }
public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) { public static boolean simpleDiffFiles(File masterFile, File testFile, int maxElementsToRead, DiffEngine.SummaryReportParams params) {
DiffEngine diffEngine = new DiffEngine(); DiffEngine diffEngine = new DiffEngine();
if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) { if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
DiffElement master = diffEngine.createDiffableFromFile(masterFile); DiffElement master = diffEngine.createDiffableFromFile(masterFile, maxElementsToRead);
DiffElement test = diffEngine.createDiffableFromFile(testFile); DiffElement test = diffEngine.createDiffableFromFile(testFile, maxElementsToRead);
List<Difference> diffs = diffEngine.diff(master, test); List<Difference> diffs = diffEngine.diff(master, test);
diffEngine.reportSummarizedDifferences(diffs, params); diffEngine.reportSummarizedDifferences(diffs, params);
return true; return true;

3
public/java/test/org/broadinstitute/sting/MD5DB.java
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@ -47,6 +47,7 @@ public class MD5DB {
/** /**
* Subdirectory under the ant build directory where we store integration test md5 results * Subdirectory under the ant build directory where we store integration test md5 results
*/ */
private static final int MAX_RECORDS_TO_READ = 10000;
public static final String LOCAL_MD5_DB_DIR = "integrationtests"; public static final String LOCAL_MD5_DB_DIR = "integrationtests";
public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests"; public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
@ -232,7 +233,7 @@ public class MD5DB {
// inline differences // inline differences
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0); DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0);
boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), params); boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
if ( success ) if ( success )
System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n", System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
pathToExpectedMD5File, pathToFileMD5File); pathToExpectedMD5File, pathToFileMD5File);