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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
This commit is contained in:
kiran 2011-02-17 23:03:46 +00:00
parent 7ffcade3c3
commit 92c82200c9
3 changed files with 16 additions and 10 deletions
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4
java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
View File

@ -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);
}
}
}
}

4
java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -571,4 +571,8 @@ public class GATKReportTable {
// Close the table
out.printf("%n");
}
public int getNumRows() {
return primaryKeyColumn.size();
}
}

18
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -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<String, String> expectations = new HashMap<String, String>();
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<String, String> 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<String, String> 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);
}