From 52c206d5db274c44da2d1d2293fd79d421236ef5 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 18 May 2012 02:32:20 -0400 Subject: [PATCH] Has anyone else ever noticed that the DiffEngine outputs were always doubled for some reason? That no longer happens with the new reports. --- .../broadinstitute/sting/gatk/report/GATKReportTable.java | 6 ------ .../sting/gatk/walkers/diffengine/DiffEngine.java | 5 ++--- .../gatk/walkers/diffengine/DiffObjectsIntegrationTest.java | 4 ++-- 3 files changed, 4 insertions(+), 11 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index 2f1b6b602..a830f8189 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -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)); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java index 28f78e880..7ce40ad98 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java @@ -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()); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java index 4a83c34cc..04fd26b14 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java @@ -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); }