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Fixed 7-PL genotypes in InbreedingCoeff tests

This commit is contained in:
meganshand 2015-09-14 09:03:17 -04:00
parent d767e1722e
commit 2507bf8d17
1 changed files with 20 additions and 20 deletions
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8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
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@ -114,14 +114,14 @@ public class InbreedingCoeffUnitTest {
//make sure that compound gets (with no ref) don't add to het count //make sure that compound gets (with no ref) don't add to het count
VariantContext test1 = makeVC("1",Arrays.asList(Aref,T,C), VariantContext test1 = makeVC("1",Arrays.asList(Aref,T,C),
makeG("s1", Aref, T, 2530, 0, 7099, 366, 3056, 14931), makeG("s1", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
makeG("s2",T,T,7099,2530,0,7099,366,3056,14931), makeG("s2", T, T, 7099, 2530, 0, 7099, 366, 3056),
makeG("s3", T, C, 7099, 2530, 7099, 3056, 0, 14931), makeG("s3", T, C, 7099, 2530, 7099, 3056, 0, 14931),
makeG("s4", Aref, T, 2530, 0, 7099, 366, 3056, 14931), makeG("s4", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
makeG("s5",T,T,7099,2530,0,7099,366,3056,14931), makeG("s5", T, T, 7099, 2530, 0, 7099, 366, 3056),
makeG("s6", Aref, T, 2530, 0, 7099, 366, 3056, 14931), makeG("s6", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
makeG("s7",T,T,7099,2530,0,7099,366,3056,14931), makeG("s7", T, T, 7099, 2530, 0, 7099, 366, 3056),
makeG("s8", Aref, T, 2530, 0, 7099, 366, 3056, 14931), makeG("s8", Aref, T, 2530, 0, 7099, 366, 3056, 14931),
makeG("s9",T,T,7099,2530,0,7099,366,3056,14931), makeG("s9", T, T, 7099, 2530, 0, 7099, 366, 3056),
makeG("s10", Aref, T, 2530, 0, 7099, 366, 3056, 14931)); makeG("s10", Aref, T, 2530, 0, 7099, 366, 3056, 14931));
final double ICresult1 = new InbreedingCoeff().calculateIC(test1, test1.getGenotypes()); final double ICresult1 = new InbreedingCoeff().calculateIC(test1, test1.getGenotypes());