From 92c82200c9998884f49692cc150106014c76a5bb Mon Sep 17 00:00:00 2001 From: kiran Date: Thu, 17 Feb 2011 23:03:46 +0000 Subject: [PATCH] Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5267 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/report/GATKReport.java | 4 +++- .../sting/gatk/report/GATKReportTable.java | 4 ++++ .../VariantEvalIntegrationTest.java | 18 +++++++++--------- 3 files changed, 16 insertions(+), 10 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java index 7e69edde3..f4c565318 100755 --- a/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +++ b/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java @@ -131,7 +131,9 @@ public class GATKReport { */ public void print(PrintStream out) { for (GATKReportTable table : tables.values()) { - table.write(out); + if (table.getNumRows() > 0) { + table.write(out); + } } } } diff --git a/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java index c66dbbdec..cbb794df0 100755 --- a/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +++ b/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java @@ -571,4 +571,8 @@ public class GATKReportTable { // Close the table out.printf("%n"); } + + public int getNumRows() { + return primaryKeyColumn.size(); + } } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index fbbfa297a..19c2ec65f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -349,7 +349,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-L 1:1-10,000,000"; for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s", - 1, Arrays.asList("4184a8d44f8c559c904e41edf464a467")); + 1, Arrays.asList("0eed0ea48cb55164ba8d9383b96811c9")); executeTestParallel("testSelect1", spec); //executeTest("testSelect1", spec); } @@ -380,8 +380,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testVESimple() { HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000", "b28516b4d3627d2eb017a5449284a4e4"); - expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "a49d897095586ddb72bfe9faf0291312"); + expectations.put("-L 1:1-10,000,000", "60bbf3539212ff4ecb172e0ef848b297"); + expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "c4a178c58464e367a5a0b22a99f35b25"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -404,9 +404,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - expectations.put("", "65d74eb7eea2355989c389e8fa886c06"); - expectations.put(" -knownName comp_hapmap -knownName dbsnp", "776827cd5a6fcaf8b8508813e8dc023c"); - expectations.put(" -knownName comp_hapmap", "e99a89cbca2027c983edc00d31ea4ec9"); + expectations.put("", "226cfe7bf3fd7d2d0325b92c5b46619d"); + expectations.put(" -knownName comp_hapmap -knownName dbsnp", "4965bd64de94b43daaa0ac2d296e9926"); + expectations.put(" -knownName comp_hapmap", "98ba082dfff25ecff506ce03126f32da"); for (String tests : testsEnumerations) { for (Map.Entry entry : expectations.entrySet()) { String extraArgs2 = entry.getKey(); @@ -424,7 +424,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("49cb4a6126c5383abd9a49a6c22b8d93")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2b969088abbfe69337fc3af663278323")); executeTestParallel("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec); } @@ -459,7 +459,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -D " + dbsnp + " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9323a6ad62dedbdb08752411960db60f")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9cc6b8df93341cf391c1cb9ad0ef6df2")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); } @@ -473,7 +473,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ef23195331affd332af1de9d261fdd0a")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("77ffc1b12bff90a993842a0eeed450ba")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); }