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Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf

This commit is contained in:
Guillermo del Angel 2011-09-13 16:57:37 -04:00
parent 07d365ce39
commit c6672f2397
2 changed files with 9 additions and 14 deletions
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19
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -175,21 +175,16 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
}
BeagleFeature beagleR2Feature = tracker.getFirstValue(beagleR2);
// ignore places where we don't have a variant
if ( beagleR2Feature == null )
return 0;
BeagleFeature beagleProbsFeature = tracker.getFirstValue(beagleProbs);
// ignore places where we don't have a variant
if ( beagleProbsFeature == null )
return 0;
BeagleFeature beaglePhasedFeature = tracker.getFirstValue(beaglePhased);
// ignore places where we don't have a variant
if ( beaglePhasedFeature == null )
return 0;
if ( beagleR2Feature == null || beagleProbsFeature == null || beaglePhasedFeature == null)
{
vcfWriter.add(vc_input);
return 1;
}
// get reference base for current position
byte refByte = ref.getBase();

4
public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"--beagleR2:BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
"--beagleProbs:BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
"--beaglePhased:BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
"-o %s -NO_HEADER", 1, Arrays.asList("3531451e84208264104040993889aaf4"));
"-o %s -NO_HEADER", 1, Arrays.asList("b445d280fd8fee1eeb4aacb3f5a54847"));
executeTest("test BeagleOutputToVCF", spec);
}
@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
"--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
"--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("8dd6ec53994fb46c5c22af8535d22965"));
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("51a57ea565176edd96d907906914b0ee"));
executeTest("testBeagleChangesSitesToRef",spec);
}