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Enable CombineGVCFs to process gVCFs that were created with basepair resolution.

This commit is contained in:
Eric Banks 2014-03-19 19:23:05 -04:00
parent 3b1c337401
commit 824983af1d
2 changed files with 12 additions and 4 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java
View File

@ -292,7 +292,7 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
// attributes // attributes
final Map<String, Object> attrs = new HashMap<>(1); final Map<String, Object> attrs = new HashMap<>(1);
if ( !USE_BP_RESOLUTION ) if ( !USE_BP_RESOLUTION && end != start )
attrs.put(VCFConstants.END_KEY, Integer.toString(end)); attrs.put(VCFConstants.END_KEY, Integer.toString(end));
// genotypes // genotypes

14
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java
View File

@ -161,16 +161,24 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
@Test @Test
public void testMD5s() throws Exception { public void testMD5s() throws Exception {
final String cmd = baseTestString(" -L 1:69485-69791"); final String cmd = baseTestString(" -L 1:69485-69791");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("aecdfa9eb32b802cd629e9f811ef15fd")); final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("c279e089fd15359e75867b1318cb4d50"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testMD5s", spec); executeTest("testMD5s", spec);
} }
@Test @Test
public void testBasepairResolution() throws Exception { public void testBasepairResolutionOutput() throws Exception {
final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution"); final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a068fb2c35cdd14df1e8f1f92f4114b4")); final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a068fb2c35cdd14df1e8f1f92f4114b4"));
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testBasepairResolution", spec); executeTest("testBasepairResolutionOutput", spec);
}
@Test
public void testBasepairResolutionInput() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("0bd914cfa16349ee0439bfa5033a4f2a"));
spec.disableShadowBCF();
executeTest("testBasepairResolutionInput", spec);
} }
} }