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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Mauricio Carneiro 2011-06-30 13:50:16 -04:00
parent efd99c3c11 804d5f22d5
commit bb6b1d615b
2 changed files with 2 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -1011,7 +1011,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
sb.append((char)b);
cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
} else {
throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed");
throw new IllegalStateException("Creating an alternate consensus from a complex indel is not allows");
}
if ( reference.length - refIdx > 0 )

2
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -19,7 +19,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("fd2d9dbf718f7a6d82ae1787ac1fe61e"));
Arrays.asList("f23ba17ee0f9573dd307708175d90cd2"));
executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(