zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -263,9 +263,6 @@ public class GATKReportTable {
* @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) {
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);
rowIdToIndex.put(ID, index);
@ -292,9 +289,6 @@ public class GATKReportTable {
* @param format the format string used to display data
*/
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());
columnInfo.add(new GATKReportColumn(columnName, format));
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
View File

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

4
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
View File

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