Class org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapserUnitTest

all > org.broadinstitute.hellbender.tools.sv.cluster > CanonicalSVCollapserUnitTest
190

tests
0

failures
0

ignored
0.070s

duration
100%

successful

Tests

Test Duration Result
collapseAlgorithmsTest[0]([[depth]], [depth]) 0s passed
collapseAlgorithmsTest[10]([[depth, pesr], [depth, pesr]], [depth, pesr]) 0.001s passed
collapseAlgorithmsTest[1]([[depth], [depth]], [depth]) 0s passed
collapseAlgorithmsTest[2]([[pesr]], [pesr]) 0s passed
collapseAlgorithmsTest[3]([[pesrA, pesrB]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[4]([[pesrB, pesrA]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[5]([[pesrA], [pesrB]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[6]([[pesrB], [pesrA]], [pesrA, pesrB]) 0.001s passed
collapseAlgorithmsTest[7]([[pesrA, pesrB], [pesrB]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[8]([[pesrB, pesrA], [pesrA]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[9]([[pesr], [depth]], [depth, pesr]) 0s passed
collapseAltAllelesTest[0]([[]], DEL, [Ljava.lang.Integer;@216fe151, [Ljava.lang.Integer;@5cdf6bb1, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@3f07eede, [Ljava.lang.Integer;@7b276a08, [<INS>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@196bc2c1, [Ljava.lang.Integer;@1fd2f96d, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@65cd37bb, [Ljava.lang.Integer;@22f79c09, [<INS:MEI>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@75f5293c, [Ljava.lang.Integer;@3f7e72a7, [], []) 0.001s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@39ae0bff, [Ljava.lang.Integer;@654e793f, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@39ee039d, [Ljava.lang.Integer;@705606ac, [], []) 0s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@1ea44b7, [Ljava.lang.Integer;@48515dfc, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@561b39f4, [Ljava.lang.Integer;@587107c, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@5d9ac1ff, [Ljava.lang.Integer;@52418721, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@7080e8fc, [Ljava.lang.Integer;@7b9e4a2a, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@9a3d0f4, [Ljava.lang.Integer;@7e130e34, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@171a6fd1, [Ljava.lang.Integer;@a929b6, [<INS:MEI>], [<INS:MEI>]) 0.001s passed
collapseAttributesTest[0]([Ljava.lang.String;@1c724957, [Ljava.lang.Object;@108ed58d, [Ljava.lang.String;@e870441, [Ljava.lang.Object;@14fe2e62, [Ljava.lang.String;@1a48f55b, [Ljava.lang.Object;@7c8c6922, OR) 0s passed
collapseAttributesTest[10]([Ljava.lang.String;@4476ac12, [Ljava.lang.Object;@447522b4, [Ljava.lang.String;@3569f0f1, [Ljava.lang.Object;@9a88a92, [Ljava.lang.String;@784fb189, [Ljava.lang.Object;@15c25cb6, OR) 0.001s passed
collapseAttributesTest[11]([Ljava.lang.String;@22e733f5, [Ljava.lang.Object;@27211dd9, [Ljava.lang.String;@2081c267, [Ljava.lang.Object;@794a3410, [Ljava.lang.String;@62a9c857, [Ljava.lang.Object;@4dc9de0e, OR) 0s passed
collapseAttributesTest[12]([Ljava.lang.String;@4b37ede0, [Ljava.lang.Object;@67f07fa1, [Ljava.lang.String;@644ae4ff, [Ljava.lang.Object;@2a080ba3, [Ljava.lang.String;@5ea4abef, [Ljava.lang.Object;@3a4ddaed, AND) 0.001s passed
collapseAttributesTest[13]([Ljava.lang.String;@18accf9c, [Ljava.lang.Object;@4ce2f4d6, [Ljava.lang.String;@58070889, [Ljava.lang.Object;@5c71329f, [Ljava.lang.String;@225fc6a2, [Ljava.lang.Object;@7940d27b, AND) 0s passed
collapseAttributesTest[14]([Ljava.lang.String;@4cd3e2f3, [Ljava.lang.Object;@10e5471d, [Ljava.lang.String;@6fc98c70, [Ljava.lang.Object;@6859080d, [Ljava.lang.String;@3bcebb8f, [Ljava.lang.Object;@1a9ce44, AND) 0.001s passed
collapseAttributesTest[15]([Ljava.lang.String;@2991524, [Ljava.lang.Object;@4cc5c43b, [Ljava.lang.String;@3d1f809, [Ljava.lang.Object;@2290186e, [Ljava.lang.String;@686a192d, [Ljava.lang.Object;@aecfc07, AND) 0.001s passed
collapseAttributesTest[16]([Ljava.lang.String;@71fa6aa7, [Ljava.lang.Object;@7d60a62f, [Ljava.lang.String;@5a7e2f07, [Ljava.lang.Object;@1bab3926, [Ljava.lang.String;@39a6c7a6, [Ljava.lang.Object;@418f5f63, AND) 0s passed
collapseAttributesTest[17]([Ljava.lang.String;@28023029, [Ljava.lang.Object;@27165978, [Ljava.lang.String;@1cd97ebe, [Ljava.lang.Object;@6431ab21, [Ljava.lang.String;@5d8b5cf6, [Ljava.lang.Object;@484313a6, AND) 0.001s passed
collapseAttributesTest[18]([Ljava.lang.String;@763960eb, [Ljava.lang.Object;@7152ee36, [Ljava.lang.String;@21dc1d99, [Ljava.lang.Object;@7bfa2d74, [Ljava.lang.String;@467924d8, [Ljava.lang.Object;@20bc417f, AND) 0s passed
collapseAttributesTest[19]([Ljava.lang.String;@4b76a0f4, [Ljava.lang.Object;@442612a6, [Ljava.lang.String;@65314e4, [Ljava.lang.Object;@a93c88a, [Ljava.lang.String;@741cb82c, [Ljava.lang.Object;@db372b, ALWAYS_FALSE) 0.001s passed
collapseAttributesTest[1]([Ljava.lang.String;@2f7765f1, [Ljava.lang.Object;@72c8af69, [Ljava.lang.String;@6d921d6b, [Ljava.lang.Object;@59464f08, [Ljava.lang.String;@4d8af13c, [Ljava.lang.Object;@7a0ebc03, OR) 0s passed
collapseAttributesTest[2]([Ljava.lang.String;@6c5fbe8a, [Ljava.lang.Object;@76c6b12c, [Ljava.lang.String;@79a7f553, [Ljava.lang.Object;@2a85e4f4, [Ljava.lang.String;@3b3fa4c0, [Ljava.lang.Object;@78333d5a, OR) 0s passed
collapseAttributesTest[3]([Ljava.lang.String;@3b5fa30d, [Ljava.lang.Object;@7d800902, [Ljava.lang.String;@1cb83205, [Ljava.lang.Object;@60af08b2, [Ljava.lang.String;@26ae9861, [Ljava.lang.Object;@5b1b5daf, OR) 0s passed
collapseAttributesTest[4]([Ljava.lang.String;@1e1c1634, [Ljava.lang.Object;@4ca3e806, [Ljava.lang.String;@4d542218, [Ljava.lang.Object;@38691f8d, [Ljava.lang.String;@463a0302, [Ljava.lang.Object;@150a201b, OR) 0s passed
collapseAttributesTest[5]([Ljava.lang.String;@9c7699e, [Ljava.lang.Object;@1ff359b7, [Ljava.lang.String;@5bbda8aa, [Ljava.lang.Object;@36d02719, [Ljava.lang.String;@46933c4, [Ljava.lang.Object;@1d2ec1f, OR) 0s passed
collapseAttributesTest[6]([Ljava.lang.String;@c3fd72, [Ljava.lang.Object;@4d7909bd, [Ljava.lang.String;@5bddb619, [Ljava.lang.Object;@b729651, [Ljava.lang.String;@14c5d220, [Ljava.lang.Object;@11f415e4, OR) 0s passed
collapseAttributesTest[7]([Ljava.lang.String;@38f0de07, [Ljava.lang.Object;@21e5feb, [Ljava.lang.String;@33742179, [Ljava.lang.Object;@6ca1c156, [Ljava.lang.String;@521f2a23, [Ljava.lang.Object;@228ed68c, OR) 0s passed
collapseAttributesTest[8]([Ljava.lang.String;@522a9876, [Ljava.lang.Object;@794ffe22, [Ljava.lang.String;@2da16d31, [Ljava.lang.Object;@74a15f4, [Ljava.lang.String;@125c443, [Ljava.lang.Object;@71d94ab, OR) 0s passed
collapseAttributesTest[9]([Ljava.lang.String;@76c1ede3, [Ljava.lang.Object;@59e938a4, [Ljava.lang.String;@323a47fe, [Ljava.lang.Object;@eb9b76c, [Ljava.lang.String;@776eedad, [Ljava.lang.Object;@6752d7fc, OR) 0s passed
collapseIntervalRepresentativeByCoordinatesTest 0.001s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@22027e62, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4d652bc6, false) 0s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4552f89f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@59b7cbec, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@9dc9212, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5b9815b6, true) 0.001s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@133acad0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7e1b96a7, true) 0s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@63c8a30e, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@26e199ed, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@49de4263, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6fa84885, true) 0.001s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2dc0cbbc, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@16b6493d, false) 0.001s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@15c4b89b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@100ed29a, true) 0s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@e0865e7, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3eb814dd, true) 0.001s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5d852761, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@106f566b, true) 0s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@12eb281f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6621ab0c, false) 0s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@77b987f3, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@46791608, false) 0s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1fb947f6, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@54d93fce, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@272600e1, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1c1b9de9, false) 0.001s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1992b8b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@16af0251, false) 0s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@d7b20d9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4b7ecd37, false) 0s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3c8802cf, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@68a1906f, false) 0.001s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2e3334d, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@66a5f996, true) 0s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1c6d65f7, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@70f446c, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4ff1e20b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@38c464df, true) 0.001s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@70ad9a9b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@300cdf3f, true) 0s passed
collapseIntervalTest[0]([Ljava.lang.String;@8c6a7db, [I@5d95c7c2, [I@40afa4f1, DEL, [I@233b5c71, [I@1e7edfb2, [I@6d26b068, [I@50931911) 0.011s passed
collapseIntervalTest[1]([Ljava.lang.String;@446b74b9, [I@41d0b71d, [I@5a4f7911, DEL, [I@1cea4fdf, [I@33b3e47, [I@47970962, [I@66b16770) 0.002s passed
collapseIntervalTest[2]([Ljava.lang.String;@72e950ef, [I@79e2aa2d, [I@13b0755e, DEL, [I@21259314, [I@19f3c1f7, [I@75acb326, [I@65263248) 0s passed
collapseIntervalTest[3]([Ljava.lang.String;@6f6d2847, [I@7fc8930f, [I@2b284acc, DUP, [I@76e5278a, [I@70cc0601, [I@4b27a3fc, [I@22b0fe7e) 0.001s passed
collapseIntervalTest[4]([Ljava.lang.String;@6ddab96c, [I@1b94df68, [I@3ef2816a, DUP, [I@71adea8d, [I@49842c0d, [I@74d6d5ca, [I@5e05f3eb) 0s passed
collapseIntervalTest[5]([Ljava.lang.String;@286e2b71, [I@6ad4d333, [I@1b3fff29, BND, [I@4f90b4c9, [I@16fc3be9, [I@5afd2f4e, [I@3e5f458f) 0s passed
collapseIntervalTest[6]([Ljava.lang.String;@377d66f, [I@30c31e10, [I@74f446ba, BND, [I@1cfca845, [I@2105c11b, [I@99e68b5, [I@5f092eaa) 0.001s passed
collapseIntervalTest[7]([Ljava.lang.String;@294c1b45, [I@53ed0519, [I@45070db0, INS, [I@13437ce5, [I@5a9ccbfb, [I@6162d87c, [I@1cf5236d) 0s passed
collapseIntervalTest[8]([Ljava.lang.String;@28261231, [I@5f709e71, [I@6a2b30b9, INS, [I@302ab67e, [I@28058dd0, [I@735d1db7, [I@4040559d) 0s passed
collapseInvalidAltAllelesTest 0.001s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@3af8f1ef, INS, 100) 0s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@393e6bdd, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@7adf0ff9, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@7d5238b4, CTX, null) 0s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@57064d38, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@4a9cb9d8, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@5bc3c4e5, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@6f53e863, CNV, 300) 0s passed
collapseSampleGenotypesTest[0](sample, [[]], [{ECN=0}], N*, [sample NA {ECN=0}]) 0.001s passed
collapseSampleGenotypesTest[10](sample, [[N*, N*], [N*, <INS>]], [{ECN=2}, {ECN=2}], N*, [sample N*/<INS> {ECN=2}]) 0s passed
collapseSampleGenotypesTest[11](sample, [[N*, N*], [N*, <INS>]], [{ECN=2, GQ=30}, {ECN=2, GQ=20}], N*, [sample N*/<INS> {ECN=2, GQ=20}]) 0s passed
collapseSampleGenotypesTest[12](sample, [[<INS>, <INS>], [N*, <INS>]], [{ECN=2}, {ECN=2}], N*, [sample N*/<INS> {ECN=2}]) 0s passed
collapseSampleGenotypesTest[13](sample, [[<INS>, <INS>], [N*, <INS>]], [{ECN=2, GQ=30}, {ECN=2, GQ=30}], N*, [sample N*/<INS> {ECN=2}]) 0.001s passed
collapseSampleGenotypesTest[14](sample, [[<INS>, <INS>], [N*, <INS>]], [{ECN=2, GQ=40}, {ECN=2, GQ=30}], N*, [sample <INS>/<INS> {ECN=2, GQ=40}]) 0s passed
collapseSampleGenotypesTest[15](sample, [[<INS>, <INS>], [N*, <INS>], [N*, N*]], [{ECN=2, GQ=30}, {ECN=2, GQ=30}, {ECN=2, GQ=30}], N*, [sample N*/<INS> {ECN=2, GQ=30}]) 0s passed
collapseSampleGenotypesTest[16](sample, [[<INS>, <INS>], [N*, <INS>], [N*, N*], [., .]], [{ECN=2, GQ=30}, {ECN=2, GQ=40}, {ECN=2, GQ=50}, {ECN=2, GQ=50}], N*, [sample N*/<INS> {ECN=2, GQ=40}]) 0.001s passed
collapseSampleGenotypesTest[17](sample, [[N*, N*, <INS>], [N*, N*, N*]], [{ECN=3}, {ECN=3}], N*, [sample N*/N*/<INS> {ECN=3}]) 0s passed
collapseSampleGenotypesTest[18](sample, [[N*, <INS>, <INS>], [N*, N*, <INS>], [N*, N*, N*]], [{ECN=3}, {ECN=3}, {ECN=3}], N*, [sample N*/N*/<INS> {ECN=3}]) 0s passed
collapseSampleGenotypesTest[19](sample, [[N*, N*, <INS>], [N*, N*, N*], [N*, <INS>, <INS>], [N*, <INS>, <INS>]], [{ECN=3}, {ECN=3}, {ECN=3}, {ECN=3}], N*, [sample N*/N*/<INS> {ECN=3}]) 0.001s passed
collapseSampleGenotypesTest[1](sample, [[]], [{ECN=0, TEST_KEY_1=test}], N*, [sample NA {ECN=0, TEST_KEY_1=test}]) 0s passed
collapseSampleGenotypesTest[20](sample, [[<INS>, <INS>, <INS>], [<INS>, <INS>, <INS>], [<INS>, <INS>, <INS>], [N*, <INS>, <INS>], [N*, <INS>, <INS>], [N*, N*, <INS>], [N*, N*, N*]], [{ECN=3}, {ECN=3}, {ECN=3}, {ECN=3}, {ECN=3}, {ECN=3}, {ECN=3}], N*, [sample N*/N*/<INS> {ECN=3}]) 0s passed
collapseSampleGenotypesTest[21](sample, [[N*], [<DEL>]], [{ECN=1, CN=1}, {ECN=1, CN=0}], N*, [sample <DEL> {CN=0, ECN=1}]) 0s passed
collapseSampleGenotypesTest[22](sample, [[N*], [.]], [{ECN=1, CN=1}, {ECN=1, CN=0}], N*, [sample N* {CN=1, ECN=1}]) 0.001s passed
collapseSampleGenotypesTest[23](sample, [[N*, N*], [N*, <DEL>]], [{ECN=2, CN=2}, {ECN=2, CN=1}], N*, [sample N*/<DEL> {CN=1, ECN=2}]) 0s passed
collapseSampleGenotypesTest[24](sample, [[N*, N*], [<DEL>, <DEL>]], [{ECN=2, CN=2}, {ECN=2, CN=0}], N*, [sample <DEL>/<DEL> {CN=0, ECN=2}]) 0s passed
collapseSampleGenotypesTest[25](sample, [[N*], [<DUP>]], [{ECN=1, CN=1}, {ECN=1, CN=2}], N*, [sample <DUP> {CN=2, ECN=1}]) 0s passed
collapseSampleGenotypesTest[26](sample, [[<DUP>], [<DUP>]], [{ECN=1, CNQ=20, CN=2}, {ECN=1, CNQ=30, CN=2}], N*, [sample <DUP> {CN=2, CNQ=30, ECN=1}]) 0s passed
collapseSampleGenotypesTest[27](sample, [[N*, N*], [N*, <DUP>]], [{ECN=2, CN=2}, {ECN=2, CN=3}], N*, [sample N*/<DUP> {CN=3, ECN=2}]) 0s passed
collapseSampleGenotypesTest[28](sample, [[N*, N*], [<DUP>, <DUP>]], [{ECN=2, CN=2}, {ECN=2, CN=4}], N*, [sample <DUP>/<DUP> {CN=4, ECN=2}]) 0s passed
collapseSampleGenotypesTest[29](sample, [[N*, N*], [N*, N*]], [{ECN=2, CN=2}, {ECN=2, CN=2}], N*, [sample N*/N* {CN=2, ECN=2}]) 0.001s passed
collapseSampleGenotypesTest[2](sample, [[.], [.]], [{ECN=1}, {ECN=1}], N*, [sample . {ECN=1}]) 0s passed
collapseSampleGenotypesTest[30](sample, [[N*, N*, N*], [N*, N*, <DUP>]], [{ECN=3, CN=3}, {ECN=3, CN=4}], N*, [sample N*/N*/<DUP> {CN=4, ECN=3}]) 0s passed
collapseSampleGenotypesTest[31](sample, [[N*, N*, N*], [N*, <DUP>, <DUP>]], [{ECN=3, CN=3}, {ECN=3, CN=5}], N*, [sample N*/<DUP>/<DUP> {CN=5, ECN=3}]) 0s passed
collapseSampleGenotypesTest[32](sample, [[N*, N*, N*], [N*, N*, <DUP>], [., ., .]], [{ECN=3, CN=3}, {ECN=3, CN=4}, {ECN=3, CN=5}], N*, [sample N*/N*/<DUP> {CN=4, ECN=3}]) 0.001s passed
collapseSampleGenotypesTest[33](sample, [[.], [.]], [{ECN=1, CN=1}, {ECN=1, CN=1}], N*, [sample . {CN=1, ECN=1}]) 0s passed
collapseSampleGenotypesTest[34](sample, [[.], [.]], [{ECN=1, CN=1}, {ECN=1, CN=2}], N*, [sample . {CN=1, ECN=1}]) 0s passed
collapseSampleGenotypesTest[35](sample, [[., .], [., .]], [{ECN=1, CNQ=30, CN=1}, {ECN=1, CNQ=30, CN=2}], N*, [sample ./. {CN=1, CNQ=30, ECN=1}]) 0s passed
collapseSampleGenotypesTest[36](sample, [[., .], [., .]], [{ECN=2, CNQ=30, CN=2}, {ECN=2, CNQ=30, CN=3}], N*, [sample ./. {CN=2, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[37](sample, [[., .], [., .]], [{ECN=2, CNQ=30, CN=2}, {ECN=2, CNQ=30, CN=1}], N*, [sample ./. {CN=2, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[38](sample, [[., .], [., .]], [{ECN=2, CNQ=30, CN=2}, {ECN=2, CNQ=30, CN=0}], N*, [sample ./. {CN=2, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[39](sample, [[., .], [., .]], [{ECN=2, CNQ=30, CN=1}, {ECN=2, CNQ=30, CN=0}], N*, [sample ./. {CN=1, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[3](sample, [[T*], [T*]], [{ECN=1}, {ECN=1}], T*, [sample T* {ECN=1}]) 0s passed
collapseSampleGenotypesTest[40](sample, [[., .], [., .]], [{ECN=2, CNQ=30, CN=5}, {ECN=2, CNQ=30, CN=6}], N*, [sample ./. {CN=5, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[41](sample, [[.], [.]], [{ECN=1, CNQ=30, CN=2}, {ECN=1, CNQ=40, CN=0}], N*, [sample . {CN=0, CNQ=40, ECN=1}]) 0s passed
collapseSampleGenotypesTest[42](sample, [[.], [.]], [{ECN=1, CNQ=50, CN=2}, {ECN=1, CNQ=40, CN=0}], N*, [sample . {CN=2, CNQ=50, ECN=1}]) 0s passed
collapseSampleGenotypesTest[43](sample, [[.], [.]], [{ECN=1, CNQ=30, CN=2}, {ECN=1, CNQ=30, CN=0}], N*, [sample . {CN=0, CNQ=30, ECN=1}]) 0.001s passed
collapseSampleGenotypesTest[44](sample, [[.], [.]], [{ECN=2, CNQ=30, CN=0}, {ECN=2, CNQ=30, CN=4}], N*, [sample . {CN=0, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[45](sample, [[.], [.]], [{ECN=2, CNQ=30, CN=1}, {ECN=2, CNQ=30, CN=3}], N*, [sample . {CN=1, CNQ=30, ECN=2}]) 0s passed
collapseSampleGenotypesTest[4](sample, [[T*], [.]], [{ECN=1}, {ECN=1}], T*, [sample T* {ECN=1}]) 0s passed
collapseSampleGenotypesTest[5](sample, [[N*, N*], [N*, N*]], [{ECN=2}, {ECN=2}], N*, [sample N*/N* {ECN=2}]) 0s passed
collapseSampleGenotypesTest[6](sample, [[N*, N*], [., .]], [{ECN=2}, {ECN=2}], N*, [sample N*/N* {ECN=2}]) 0.001s passed
collapseSampleGenotypesTest[7](sample, [[N*], [<INS>]], [{ECN=1}, {ECN=1}], N*, [sample <INS> {ECN=1}]) 0s passed
collapseSampleGenotypesTest[8](sample, [[.], [<INS>]], [{ECN=1, GQ=30}, {ECN=1, GQ=20}], N*, [sample <INS> {ECN=1, GQ=20}]) 0s passed
collapseSampleGenotypesTest[9](sample, [[<INS>], [<INS>]], [{ECN=1, GQ=20}, {ECN=1, GQ=30}], N*, [sample <INS> {ECN=1, GQ=30}]) 0s passed
collapseTypesTest[0]([DEL], DEL) 0s passed
collapseTypesTest[10]([INV, INV], INV) 0s passed
collapseTypesTest[11]([BND, BND], BND) 0s passed
collapseTypesTest[12]([CNV, CNV], CNV) 0s passed
collapseTypesTest[13]([DEL, DUP, CNV], CNV) 0s passed
collapseTypesTest[1]([DUP], DUP) 0s passed
collapseTypesTest[2]([INS], INS) 0.001s passed
collapseTypesTest[3]([INV], INV) 0s passed
collapseTypesTest[4]([BND], BND) 0s passed
collapseTypesTest[5]([CNV], CNV) 0s passed
collapseTypesTest[6]([DEL, DUP], CNV) 0s passed
collapseTypesTest[7]([DEL, DEL], DEL) 0s passed
collapseTypesTest[8]([DUP, DUP], DUP) 0s passed
collapseTypesTest[9]([INS, INS], INS) 0s passed
getMostPreciseCallsTest[0]([Ljava.lang.String;@35570a84, [[depth]], [depth1]) 0.001s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@2af781f3, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@4b7272d6, [[pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@749330a8, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@2f71bb66, [[depth], [pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@207512c3, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@56c72fff, [[depth, pesr], [pesr]], [pesr1, mixed1]) 0s passed
makeBiallelicListTest[0](<DEL>, A*, 0, 0, []) 0s passed
makeBiallelicListTest[1](<DEL>, A*, 0, 1, [A*]) 0.001s passed
makeBiallelicListTest[2](<DEL>, A*, 1, 1, [<DEL>]) 0s passed
makeBiallelicListTest[3](<INS>, A*, 1, 1, [<INS>]) 0s passed
makeBiallelicListTest[4](<DEL>, A*, 1, 2, [A*, <DEL>]) 0s passed
makeBiallelicListTest[5](<DEL>, A*, 2, 2, [<DEL>, <DEL>]) 0s passed
makeBiallelicListTest[6](<DEL>, A*, 2, 2, [<DEL>, <DEL>]) 0s passed
makeBiallelicListTest[7](<DEL>, A*, 2, 3, [A*, <DEL>, <DEL>]) 0.001s passed
testCollapseRefAlleles[0](1, N*) 0s passed
testCollapseRefAlleles[1](100000, C*) 0s passed
testCollapseRefAlleles[2](100001, A*) 0s passed
testCollapseRefAlleles[3](100002, C*) 0s passed
testCollapseRefAlleles[4](100003, T*) 0s passed
testCollapseRefAlleles[5](248956422, N*) 0s passed
testCollapse[0](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@5634f627, org.broadinstitute.hellbender.tools.sv.SVCallRecord@380ea757) 0.001s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@2e43fc06, org.broadinstitute.hellbender.tools.sv.SVCallRecord@5fb7b227) 0s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@12aa9370, org.broadinstitute.hellbender.tools.sv.SVCallRecord@2338eeef) 0.004s passed
testComplexSubtypeAndIntervals 0.009s passed
testConstructBndAllele[0](true, true, contigB, 10, A, A]contigB:10]) 0s passed
testConstructBndAllele[1](true, false, contigB, 10, T, T[contigB:10[) 0s passed
testConstructBndAllele[2](false, true, contigB, 20, C, ]contigB:20]C) 0.003s passed
testConstructBndAllele[3](false, false, contigB, 20, G, [contigB:20[G) 0s passed
testGetDistance[0](5, 10, [I@2295535f, [I@188f626a, 15) 0s passed
testGetDistance[1](5, 10, [I@75ba33b8, [I@7d3d89fb, 5) 0s passed
testGetDistance[2](5, 10, [I@62b71cfa, [I@46b4d4e7, 10) 0s passed
testGetDistance[3](5, 10, [I@58da6f7d, [I@2d0f850, 0) 0s passed
testGetDistance[4](5, 10, [I@a6017f9, [I@14a204f, 11) 0s passed
testGetDistance[5](0, 0, [I@7e3ccedb, [I@7469d13a, 0) 0s passed
testGetDistance[6](-5, -10, [I@4a907e5a, [I@52c22bc5, 11) 0s passed
testHarmonizeAltAlleles[0]([<DEL>], [[null A*/<DEL>]], null) 0s passed
testHarmonizeAltAlleles[1]([<DEL>], [[null A*/A*]], null) 0.001s passed
testHarmonizeAltAlleles[2]([], [[null A*/A*]], null) 0s passed
testHarmonizeAltAlleles[3]([<DEL>, <DUP>], [[null A*/<DEL>]], null) 0s passed
testHarmonizeAltAlleles[4]([<DEL>, <DUP>], [[null A*/A*]], null) 0s passed
testHarmonizeAltAlleles[5]([<DEL>, <DUP>], [[null A*/<DEL>], [null A*/<DUP>]], null) 0.001s passed
testHarmonizeAltAlleles[6]([<DUP>], [[null A*/<DUP:TANDEM>]], [[null A*/<DUP>]]) 0s passed
testHarmonizeAltAlleles[7]([<DUP:TANDEM>], [[null A*/<DUP>]], [[null A*/<DUP:TANDEM>]]) 0s passed
testHarmonizeAltAlleles[8]([<DUP:TANDEM>], [[null A*/<DUP>], [null A*/<DUP:TANDEM>]], [[null A*/<DUP:TANDEM>], [null A*/<DUP:TANDEM>]]) 0s passed
testHarmonizeAltAlleles[9]([<INS:MEI>], [[null A*/<INS>], [null A*/<INS:MEI>]], [[null A*/<INS:MEI>], [null A*/<INS:MEI>]]) 0.001s passed