diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java index 4ec966bf5..dfacb6a20 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java @@ -40,17 +40,21 @@ public class ValidationDataAnalysis extends BasicVariantAnalysis implements Geno calls_at_validated_sites++; } } - out.println(context.getLocation()); + //out.println(context.getLocation()); - return ""; + return null; } public List done() { List s = new ArrayList(); - s.add(String.format("validated sites %d", validated_sites)); - s.add(String.format("calls at validated sites %d", calls_at_sites_validated_true)); - s.add(String.format("calls at sites validated true %d", calls_at_validated_sites)); - s.add(String.format("%% validated true %f", (float) calls_at_validated_sites / calls_at_sites_validated_true)); + if (calls_at_validated_sites > 0) { // only output info if there were any validation sites encountered + s.add(String.format("validated sites %d", validated_sites)); + s.add(String.format("calls at validated sites %d", calls_at_validated_sites)); + s.add(String.format("calls at sites validated true %d", calls_at_sites_validated_true)); + s.add(String.format("%% validated true %f", (float) calls_at_validated_sites / calls_at_sites_validated_true)); + }else{ + s.add("No validation data encountered"); + } return s; } } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java index f4dbaabad..e064b05f2 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java @@ -19,7 +19,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantROD() { List md5 = new ArrayList(); - md5.add("7d1f8ddbf2d2f721a0c6dc39c97b584c"); + md5.add("86582b57ec27dd9c4a6e0252eb010376"); /** * the above MD5 was calculated from running the following command: @@ -50,7 +50,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantRODConfSix() { List md5 = new ArrayList(); - md5.add("27969a841874fc00d007b01ee008eb58"); + md5.add("875dea21073bb5b24a771105bdeb2225"); /** * the above MD5 was calculated from running the following command: @@ -82,7 +82,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalVariantRODOutputViolations() { List md5 = new ArrayList(); - md5.add("63940f8d977b15bb1bcc9223ebeacf43"); + md5.add("ad2ca71dfa7e45f369380178c4f8e69f"); /** * the above MD5 was calculated from running the following command: @@ -114,7 +114,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalGenotypeROD() { List md5 = new ArrayList(); - md5.add("c616348c1041157acd2715285c5b38b8"); + md5.add("46c381dad05310267cdfd409228d3692"); /** * the above MD5 was calculated after running the following command: * @@ -148,7 +148,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { @Test public void testEvalMarksGenotypingExample() { List md5 = new ArrayList(); - md5.add("004cdf0c3ca46744daf42645785acc28"); + md5.add("cb914e7b65e6561685cccf0cd2cc5dfb"); /** * Run with the following commands: *