Class org.broadinstitute.hellbender.testutils.VariantContextTestUtilsUnitTest

all > org.broadinstitute.hellbender.testutils > VariantContextTestUtilsUnitTest
46

tests
0

failures
0

ignored
0.109s

duration
100%

successful

Tests

Test Duration Result
testARemapping[0]([1, 2, 3], [2, 3, 1], [0, 2, 3, 1]) 0.001s passed
testARemapping[1]([1, 2, 3], [1, 2, 3], [0, 1, 2, 3]) 0s passed
testARemapping[2]([a, b, c], [c, b, a], [0, 3, 2, 1]) 0s passed
testASRemapping[0]([1, 2, 3, 4], [1, 3, 4, 2], [0, 2, 3, 1]) 0s passed
testASRemapping[1]([1, 2, 3, 4], [1, 2, 3, 4], [0, 1, 2, 3]) 0s passed
testASRemapping[2]([a, b, c, d], [a, d, c, b], [0, 3, 2, 1]) 0s passed
testAttributeExistenceCheck 0.002s passed
testGListsToRemap[0]([0, 1, 2], [2, 1, 0], [A*, T], [T, A*], 2) 0.006s passed
testGListsToRemap[1]([0, 1, 2, 3, 4, 5], [2, 1, 0, 4, 3, 5], [A*, T, C], [T, A*, C], 2) 0s passed
testNormalizeInteger[0](27, 27) 0s passed
testNormalizeInteger[10](-21.72, -21.72) 0s passed
testNormalizeInteger[11](10, 10) 0s passed
testNormalizeInteger[12](SomeValue, SomeValue) 0s passed
testNormalizeInteger[13](java.lang.Object@783905c2, java.lang.Object@783905c2) 0s passed
testNormalizeInteger[1](-27, -27) 0s passed
testNormalizeInteger[2](0, 0) 0s passed
testNormalizeInteger[3](-27014, -27014) 0s passed
testNormalizeInteger[4](1, 1) 0s passed
testNormalizeInteger[5](1, 1) 0s passed
testNormalizeInteger[6](-1, -1) 0s passed
testNormalizeInteger[7](1, 1) 0s passed
testNormalizeInteger[8](-2.172e+00, -2.172e+00) 0s passed
testNormalizeInteger[9](-2.172, -2.172) 0s passed
testNormalizeScientificNotation[0](-2.172e+00, -2.172) 0s passed
testNormalizeScientificNotation[1](-2.172, -2.172) 0s passed
testNormalizeScientificNotation[2](-2.172e+01, -21.72) 0s passed
testNormalizeScientificNotation[3](-21.72, -21.72) 0s passed
testNormalizeScientificNotation[4](10, 10) 0s passed
testNormalizeScientificNotation[5](SomeValue, SomeValue) 0s passed
testNormalizeScientificNotation[6](java.lang.Object@6546f3f0, java.lang.Object@6546f3f0) 0s passed
testOrderSortAlleles[0]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[] filters=, true) 0.005s passed
testOrderSortAlleles[1]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, T] attr={} GT=[] filters=, false) 0s passed
testOrderSortAlleles[2]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[] filters=, true) 0.002s passed
testOrderSortAlleles[3]([VC a @ 20:10433328 Q. of type=MIXED alleles=[A*, C, CC, G, GG] attr={AS_RAW_MQ=0|1|2|3|4} GT=[] filters=, [VC a @ 20:10433328 Q. of type=MIXED alleles=[A*, C, CC, G, GG] attr={AS_RAW_MQ=0|4|1|3|2} GT=[] filters=, true) 0s passed
testOrderSortAlleles[4]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|10, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[] filters=, false) 0.001s passed
testOrderSortAlleles[5]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[] filters=, false) 0.001s passed
testOrderSortAlleles[6]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,2,3 PL 1600,1900,0,1900,1900,1900],[NA2 C/G GQ 30 AD 3,4,5 PL 500,400,300,200,100,0]] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,3,2 PL 1600,1900,1900,1900,1900,0],[NA2 C/G GQ 30 AD 3,5,4 PL 500,200,0,400,100,300]] filters=, true) 0.006s passed
testOrderSortAlleles[7]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,2,3 PL 1600,1900,0,1900,1900,1900],[NA2 C/G GQ 30 AD 3,4,5 PL 500,400,300,200,100,0]] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,3,2 PL 1600,1900,1900,1900,1900,0],[NA2 C/G GQ 40 AD 3,5,4 PL 500,200,0,400,100,300]] filters=, false) 0.002s passed
testOrderSortAlleles[8]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,2,3 PL 1600,1900,0,1900,1900,1900],[NA2 C/G GQ 30 AD 3,4,5 PL 500,400,300,200,100,0]] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,3,2 PL 1600,1900,0,1900,1900,1900],[NA2 C/G GQ 30 AD 3,5,4 PL 500,400,300,200,100,0]] filters=, false) 0.001s passed
testOrderSortAlleles[9]([VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|20|10, PG=10,20,30,40,50,60, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,2,3 PL 1600,1900,0,1900,1900,1900],[NA2 C/G GQ 30 AD 3,4,5 PL 500,400,300,200,100,0]] filters=, [VC a @ 20:10433328 Q. of type=SNP alleles=[A*, C, G] attr={AS_RAW_MQ=40|10|20, PG=10,40,60,20,50,30, RAW_MQ=20} GT=[[NA1 A*/G GQ 30 AD 1,3,2 PL 1600,1900,1900,1900,1900,0],[NA2 C/G GQ 30 AD 3,4,4 PL 500,200,0,400,100,300]] filters=, false) 0.002s passed
testReadEntireVCFIntoMemoryNonExistentFile 0s passed
testReadEntireVCFIntoMemoryNonVCFInput 0.002s passed
testReadEntireVCFIntoMemory[0](/gatkCloneMountPoint/src/test/resources/large/dbsnp_138.b37.20.21.vcf, 160, 9594) 0.078s passed
testRemapping[0]([1, 2, 3, 4], [1, 3, 4, 2], [0, 2, 3, 1]) 0s passed
testRemapping[1]([1, 2, 3, 4], [1, 2, 3, 4], [0, 1, 2, 3]) 0s passed
testRemapping[2]([a, b, c, d], [a, d, c, b], [0, 3, 2, 1]) 0s passed

Standard error

20:25:28.891 INFO  FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/large/dbsnp_138.b37.20.21.vcf
20:25:28.970 INFO  FeatureManager - Using codec BEDCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/engine/example_features.bed