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

Updated integration tests for VariantEval. Hooray for IT! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1866 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-10-16 20:00:29 +00:00
parent 41a95cb3f0
commit bdb34fcf38
2 changed files with 15 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java
View File

@ -40,17 +40,21 @@ public class ValidationDataAnalysis extends BasicVariantAnalysis implements Geno
calls_at_validated_sites++; calls_at_validated_sites++;
} }
} }
out.println(context.getLocation()); //out.println(context.getLocation());
return ""; return null;
} }
public List<String> done() { public List<String> done() {
List<String> s = new ArrayList<String>(); List<String> s = new ArrayList<String>();
s.add(String.format("validated sites %d", validated_sites)); if (calls_at_validated_sites > 0) { // only output info if there were any validation sites encountered
s.add(String.format("calls at validated sites %d", calls_at_sites_validated_true)); s.add(String.format("validated sites %d", validated_sites));
s.add(String.format("calls at sites validated true %d", calls_at_validated_sites)); s.add(String.format("calls at validated sites %d", calls_at_validated_sites));
s.add(String.format("%% validated true %f", (float) calls_at_validated_sites / calls_at_sites_validated_true)); 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; return s;
} }
} }

10
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
View File

@ -19,7 +19,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test @Test
public void testEvalVariantROD() { public void testEvalVariantROD() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("7d1f8ddbf2d2f721a0c6dc39c97b584c"); md5.add("86582b57ec27dd9c4a6e0252eb010376");
/** /**
* the above MD5 was calculated from running the following command: * the above MD5 was calculated from running the following command:
@ -50,7 +50,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test @Test
public void testEvalVariantRODConfSix() { public void testEvalVariantRODConfSix() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("27969a841874fc00d007b01ee008eb58"); md5.add("875dea21073bb5b24a771105bdeb2225");
/** /**
* the above MD5 was calculated from running the following command: * the above MD5 was calculated from running the following command:
@ -82,7 +82,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test @Test
public void testEvalVariantRODOutputViolations() { public void testEvalVariantRODOutputViolations() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("63940f8d977b15bb1bcc9223ebeacf43"); md5.add("ad2ca71dfa7e45f369380178c4f8e69f");
/** /**
* the above MD5 was calculated from running the following command: * the above MD5 was calculated from running the following command:
@ -114,7 +114,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test @Test
public void testEvalGenotypeROD() { public void testEvalGenotypeROD() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("c616348c1041157acd2715285c5b38b8"); md5.add("46c381dad05310267cdfd409228d3692");
/** /**
* the above MD5 was calculated after running the following command: * the above MD5 was calculated after running the following command:
* *
@ -148,7 +148,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test @Test
public void testEvalMarksGenotypingExample() { public void testEvalMarksGenotypingExample() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("004cdf0c3ca46744daf42645785acc28"); md5.add("cb914e7b65e6561685cccf0cd2cc5dfb");
/** /**
* Run with the following commands: * Run with the following commands:
* *