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There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5136 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-31 15:05:45 +00:00
parent f8609afd4e
commit d406d9b3fc
2 changed files with 3 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -206,7 +206,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
/** /**
* Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key * Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key
*/ */
if ( (isValidation && prior < 0.0) || genotype.isCalled() && genotype.hasLikelihoods()) { if ( (isValidation && prior < 0.0) || genotype.hasLikelihoods() ) {
double[] likeArray = genotype.getLikelihoods().getAsVector(); double[] likeArray = genotype.getLikelihoods().getAsVector();
if( isMaleOnChrX ) { if( isMaleOnChrX ) {
likeArray[1] = -255; likeArray[1] = -255;
@ -228,7 +228,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
} }
} }
if (beagleGenotypesWriter != null) { if ( beagleGenotypesWriter != null && genotype.isCalled() ) {
char a = genotype.getAllele(0).toString().charAt(0); char a = genotype.getAllele(0).toString().charAt(0);
char b = genotype.getAllele(0).toString().charAt(0); char b = genotype.getAllele(0).toString().charAt(0);

2
java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -50,7 +50,7 @@ public class BeagleIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
"-T ProduceBeagleInput -R " + hg19Reference + " " + "-T ProduceBeagleInput -R " + hg19Reference + " " +
"-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-o %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e")); "-o %s", 1, Arrays.asList("a01c704246f3dd1b9c65774007e51e69"));
executeTest("test BeagleInput", spec); executeTest("test BeagleInput", spec);
} }