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Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-05-23 21:32:53 +00:00
parent bc4305c956
commit 4bfec4c55b
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
View File

@ -108,7 +108,7 @@ public class SAMPileupCodec implements FeatureCodec<SAMPileupFeature> {
if ( feature.getRef() == '*' ) { if ( feature.getRef() == '*' ) {
parseIndels(observedString,feature) ; parseIndels(observedString,feature) ;
if ( feature.isDeletion() ) feature.setEnd(feature.getStart()+feature.length()-1); if ( feature.isDeletion() ) feature.setEnd(feature.getStart()+feature.length()-1);
else feature.setEnd(feature.getStart()-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!! else feature.setEnd(feature.getStart()); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!!
} else { } else {
parseBasesAndQuals(feature,tokens[8],tokens[9]); parseBasesAndQuals(feature,tokens[8],tokens[9]);
// if the variant is a SNP or a reference base (i.e. no variant at all) // if the variant is a SNP or a reference base (i.e. no variant at all)

4
java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java
View File

@ -12,14 +12,14 @@ import java.util.Collections;
* @version 0.1 * @version 0.1
*/ */
public class ValidatingPileupIntegrationTest extends WalkerTest { public class ValidatingPileupIntegrationTest extends WalkerTest {
@Test(enabled = false) @Test(enabled = true)
public void testEcoliThreaded() { public void testEcoliThreaded() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T ValidatingPileup" + "-T ValidatingPileup" +
" -I " + validationDataLocation + "MV1994.selected.bam" + " -I " + validationDataLocation + "MV1994.selected.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" + " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" + " -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +
" -S SILENT -nt 8 -U ALLOW_SEQ_DICT_INCOMPATIBILITY",0, Collections.<String>emptyList()); " -S SILENT -nt 8",0, Collections.<String>emptyList());
executeTest("testEcoliThreaded",spec); executeTest("testEcoliThreaded",spec);
} }
} }