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Correct errant array element swap in FAM file output. 

dad and mom are swapped; paternal first, then maternal

updated MD5 chksums for test files

remove commented lines
This commit is contained in:
Joseph White 2015-04-26 16:17:41 -04:00
parent f77cee5171
commit abb6bc6f57
2 changed files with 8 additions and 4 deletions
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8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
View File

@ -92,7 +92,9 @@ public class VariantsToBinaryPedIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("NA12878.subset.vcf", "CEUTrio.NA12878.fam",10), baseTestString("NA12878.subset.vcf", "CEUTrio.NA12878.fam",10),
3, 3,
Arrays.asList("411ef932095728bfa5e509c2c0e4cfa8","daf853d2fcbfc77daa1f9ae190be24f4","02f1c462ebc8576e399d0e94f729fd95") Arrays.asList("411ef932095728bfa5e509c2c0e4cfa8",
"98f955f8b2af0aef58c96cc0cde66662",
"02f1c462ebc8576e399d0e94f729fd95")
); );
executeTest(testName, spec); executeTest(testName, spec);
@ -182,7 +184,9 @@ public class VariantsToBinaryPedIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("CEUTrio.subset.vcf", "CEUTrio.fam",10), baseTestString("CEUTrio.subset.vcf", "CEUTrio.fam",10),
3, 3,
Arrays.asList("59b93fbb4bb31309b3adc83ba96dd1a2","3bfb01c17935e3d194d266755b446e82","7887d2e0bf605dbcd0688c552cdb99d5") Arrays.asList("59b93fbb4bb31309b3adc83ba96dd1a2",
"cbef0432e78f0a31a3cb4cd1942ada62",
"7887d2e0bf605dbcd0688c552cdb99d5")
); );
executeTest(testName, spec); executeTest(testName, spec);

4
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
View File

@ -488,8 +488,8 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
} }
String sid = famSplit[1]; String sid = famSplit[1];
String fid = famSplit[0]; String fid = famSplit[0];
String mom = famSplit[2]; String dad = famSplit[2];
String dad = famSplit[3]; String mom = famSplit[3];
String sex = famSplit[4]; String sex = famSplit[4];
String pheno = famSplit[5]; String pheno = famSplit[5];
HashMap<String,String> values = new HashMap<String, String>(); HashMap<String,String> values = new HashMap<String, String>();