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Has anyone else ever noticed that the DiffEngine outputs were always doubled for some reason? That no longer happens with the new reports.

This commit is contained in:
Eric Banks 2012-05-18 02:32:20 -04:00
parent 03d40272c8
commit 52c206d5db
3 changed files with 4 additions and 11 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -263,9 +263,6 @@ public class GATKReportTable {
* @param populateFirstColumn should we automatically populate the first column with the row's ID? * @param populateFirstColumn should we automatically populate the first column with the row's ID?
*/ */
public void addRowIDMapping(final Object ID, final int index, final boolean populateFirstColumn) { public void addRowIDMapping(final Object ID, final int index, final boolean populateFirstColumn) {
if ( populateFirstColumn && !isValidName(ID.toString()) )
throw new ReviewedStingException("Attempted to set a GATKReportTable ID of '" + ID + "'; GATKReportTable IDs must be purely alphanumeric - no spaces or special characters are allowed.");
expandTo(index, false); expandTo(index, false);
rowIdToIndex.put(ID, index); rowIdToIndex.put(ID, index);
@ -292,9 +289,6 @@ public class GATKReportTable {
* @param format the format string used to display data * @param format the format string used to display data
*/ */
public void addColumn(String columnName, String format) { public void addColumn(String columnName, String format) {
if (!isValidName(columnName)) {
throw new ReviewedStingException("Attempted to set a GATKReportTable column name of '" + columnName + "'. GATKReportTable column names must be purely alphanumeric - no spaces or special characters are allowed.");
}
columnNameToIndex.put(columnName, columnInfo.size()); columnNameToIndex.put(columnName, columnInfo.size());
columnInfo.add(new GATKReportColumn(columnName, format)); columnInfo.add(new GATKReportColumn(columnName, format));
} }

5
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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@ -240,10 +240,9 @@ public class DiffEngine {
table.addColumn("Difference"); table.addColumn("Difference");
table.addColumn("NumberOfOccurrences"); table.addColumn("NumberOfOccurrences");
table.addColumn("ExampleDifference"); table.addColumn("ExampleDifference");
for ( int i = 0; i > toShow.size(); i++ ) { for ( final Difference diff : toShow ) {
final Difference diff = toShow.get(i);
final String key = diff.getPath(); final String key = diff.getPath();
table.addRowIDMapping(key, i, true); table.addRowID(key, true);
table.set(key, "NumberOfOccurrences", diff.getCount()); table.set(key, "NumberOfOccurrences", diff.getCount());
table.set(key, "ExampleDifference", diff.valueDiffString()); table.set(key, "ExampleDifference", diff.valueDiffString());
} }

4
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
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@ -50,8 +50,8 @@ public class DiffObjectsIntegrationTest extends WalkerTest {
@DataProvider(name = "data") @DataProvider(name = "data")
public Object[][] createData() { public Object[][] createData() {
new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "dba5eab2b9587c1062721b164e4fd9a6"); new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "aeb2283178d162555de18524fb127c84");
new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "de35c93450b46db5fc5516af3c55d62a"); new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "a43f6f2e209efe2d754c4d2104ca2156");
return TestParams.getTests(TestParams.class); return TestParams.getTests(TestParams.class);
} }