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

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

tests
0

failures
0

ignored
0.065s

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]) 0s 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;@776eedad, [Ljava.lang.Integer;@6752d7fc, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@4cd3e2f3, [Ljava.lang.Integer;@10e5471d, [<INS>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@2220780d, [Ljava.lang.Integer;@2991524, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@3d1f809, [Ljava.lang.Integer;@2290186e, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@3569f0f1, [Ljava.lang.Integer;@9a88a92, [], []) 0s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@15c25cb6, [Ljava.lang.Integer;@6fd6d887, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@27211dd9, [Ljava.lang.Integer;@2081c267, [], []) 0s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@62a9c857, [Ljava.lang.Integer;@4dc9de0e, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@4b37ede0, [Ljava.lang.Integer;@67f07fa1, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@2a080ba3, [Ljava.lang.Integer;@5ea4abef, [<DEL>], [<DEL>]) 0.001s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@993bc47, [Ljava.lang.Integer;@632cfbc5, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@4ce2f4d6, [Ljava.lang.Integer;@58070889, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@225fc6a2, [Ljava.lang.Integer;@7940d27b, [<INS:MEI>], [<INS:MEI>]) 0.001s passed
collapseAttributesTest[0]([Ljava.lang.String;@aecfc07, [Ljava.lang.Object;@6f14ce3, [Ljava.lang.String;@2400673b, [Ljava.lang.Object;@1c1bb1e7, [Ljava.lang.String;@71fa6aa7, [Ljava.lang.Object;@7d60a62f, OR) 0.001s passed
collapseAttributesTest[10]([Ljava.lang.String;@2b75b77d, [Ljava.lang.Object;@4552f89f, [Ljava.lang.String;@59b7cbec, [Ljava.lang.Object;@f9402c2, [Ljava.lang.String;@9dc9212, [Ljava.lang.Object;@5b9815b6, OR) 0s passed
collapseAttributesTest[11]([Ljava.lang.String;@133acad0, [Ljava.lang.Object;@7e1b96a7, [Ljava.lang.String;@65b51977, [Ljava.lang.Object;@63c8a30e, [Ljava.lang.String;@26e199ed, [Ljava.lang.Object;@46d8d38, OR) 0s passed
collapseAttributesTest[12]([Ljava.lang.String;@6fa84885, [Ljava.lang.Object;@452c8a6c, [Ljava.lang.String;@2dc0cbbc, [Ljava.lang.Object;@16b6493d, [Ljava.lang.String;@3bf7c70e, [Ljava.lang.Object;@1aa945f6, AND) 0s passed
collapseAttributesTest[13]([Ljava.lang.String;@100ed29a, [Ljava.lang.Object;@4058b398, [Ljava.lang.String;@e0865e7, [Ljava.lang.Object;@3eb814dd, [Ljava.lang.String;@58c48b92, [Ljava.lang.Object;@5d852761, AND) 0.001s passed
collapseAttributesTest[14]([Ljava.lang.String;@6e8fa647, [Ljava.lang.Object;@12eb281f, [Ljava.lang.String;@6621ab0c, [Ljava.lang.Object;@c1765ad, [Ljava.lang.String;@1fb947f6, [Ljava.lang.Object;@54d93fce, AND) 0s passed
collapseAttributesTest[15]([Ljava.lang.String;@8c6a7db, [Ljava.lang.Object;@5d95c7c2, [Ljava.lang.String;@40afa4f1, [Ljava.lang.Object;@233b5c71, [Ljava.lang.String;@1e7edfb2, [Ljava.lang.Object;@6d26b068, AND) 0s passed
collapseAttributesTest[16]([Ljava.lang.String;@19a48bde, [Ljava.lang.Object;@5137526a, [Ljava.lang.String;@684138c5, [Ljava.lang.Object;@6724f10e, [Ljava.lang.String;@5a637c4f, [Ljava.lang.Object;@312cc16b, AND) 0s passed
collapseAttributesTest[17]([Ljava.lang.String;@1026770d, [Ljava.lang.Object;@5166f042, [Ljava.lang.String;@616549c, [Ljava.lang.Object;@45a824d, [Ljava.lang.String;@27e713d4, [Ljava.lang.Object;@41e5038a, AND) 0s passed
collapseAttributesTest[18]([Ljava.lang.String;@257ba195, [Ljava.lang.Object;@3a9d6f5d, [Ljava.lang.String;@530dd2d7, [Ljava.lang.Object;@3e6f3ad5, [Ljava.lang.String;@46e05384, [Ljava.lang.Object;@17563b82, AND) 0s passed
collapseAttributesTest[19]([Ljava.lang.String;@6d0ef6dc, [Ljava.lang.Object;@2936f48a, [Ljava.lang.String;@f1a5005, [Ljava.lang.Object;@23001753, [Ljava.lang.String;@39a2adf9, [Ljava.lang.Object;@27ae8ce3, ALWAYS_FALSE) 0s passed
collapseAttributesTest[1]([Ljava.lang.String;@1bab3926, [Ljava.lang.Object;@39a6c7a6, [Ljava.lang.String;@418f5f63, [Ljava.lang.Object;@6a225642, [Ljava.lang.String;@28023029, [Ljava.lang.Object;@27165978, OR) 0s passed
collapseAttributesTest[2]([Ljava.lang.String;@6431ab21, [Ljava.lang.Object;@5d8b5cf6, [Ljava.lang.String;@484313a6, [Ljava.lang.Object;@1fb8b89e, [Ljava.lang.String;@763960eb, [Ljava.lang.Object;@7152ee36, OR) 0s passed
collapseAttributesTest[3]([Ljava.lang.String;@7bfa2d74, [Ljava.lang.Object;@467924d8, [Ljava.lang.String;@20bc417f, [Ljava.lang.Object;@614da024, [Ljava.lang.String;@4b76a0f4, [Ljava.lang.Object;@442612a6, OR) 0.001s passed
collapseAttributesTest[4]([Ljava.lang.String;@a93c88a, [Ljava.lang.Object;@741cb82c, [Ljava.lang.String;@db372b, [Ljava.lang.Object;@1e31e7e0, [Ljava.lang.String;@a72bb34, [Ljava.lang.Object;@1bbebf8e, OR) 0s passed
collapseAttributesTest[5]([Ljava.lang.String;@539a50ea, [Ljava.lang.Object;@4caeeab6, [Ljava.lang.String;@22027e62, [Ljava.lang.Object;@4d652bc6, [Ljava.lang.String;@4cf93f80, [Ljava.lang.Object;@77b987f3, OR) 0s passed
collapseAttributesTest[6]([Ljava.lang.String;@22263e1a, [Ljava.lang.Object;@272600e1, [Ljava.lang.String;@1c1b9de9, [Ljava.lang.Object;@125c1134, [Ljava.lang.String;@1992b8b, [Ljava.lang.Object;@16af0251, OR) 0s passed
collapseAttributesTest[7]([Ljava.lang.String;@243c4ffe, [Ljava.lang.Object;@6c31ed81, [Ljava.lang.String;@2e2d7dc, [Ljava.lang.Object;@d7b20d9, [Ljava.lang.String;@4b7ecd37, [Ljava.lang.Object;@28c06c3c, OR) 0s passed
collapseAttributesTest[8]([Ljava.lang.String;@68a1906f, [Ljava.lang.Object;@558bff39, [Ljava.lang.String;@7e01d838, [Ljava.lang.Object;@2e3334d, [Ljava.lang.String;@66a5f996, [Ljava.lang.Object;@6cddb04c, OR) 0s passed
collapseAttributesTest[9]([Ljava.lang.String;@70f446c, [Ljava.lang.Object;@4e2f6452, [Ljava.lang.String;@4ff1e20b, [Ljava.lang.Object;@38c464df, [Ljava.lang.String;@45957b8f, [Ljava.lang.Object;@70ad9a9b, OR) 0s passed
collapseIntervalRepresentativeByCoordinatesTest 0.001s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@36dd68f1, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4da929ef, false) 0.001s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6a4f3df4, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4d76f990, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1e6a74fe, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@d594a5a, true) 0s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@72216f0b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3fa13835, true) 0s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@438f205c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3a2f4611, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@19710bd9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@23c6556b, true) 0s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@222e4377, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3310bb28, false) 0.001s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6bc6400e, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2f0765f7, true) 0s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@51e513b7, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@87affb5, true) 0.001s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@518e6d6c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@280fa441, true) 0s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5be17e53, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@79a68d4e, false) 0.001s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@75910e0e, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@28566aad, false) 0s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@60483dcf, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@308bd473, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@29c8a858, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@54543211, false) 0s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@45b244c4, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2954be42, false) 0.001s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5b1e336c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5fc3333f, false) 0s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3579682, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@297840d7, false) 0s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@52d1bb9c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@39c437e9, true) 0s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@735ed1d2, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2c8c897e, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@a9b5c85, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@fcecc45, true) 0.001s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@f25176a, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5f8a0d7f, true) 0s passed
collapseIntervalTest[0]([Ljava.lang.String;@2114955c, [I@1362f4, [I@6e5506c9, DEL, [I@446b74b9, [I@41d0b71d, [I@5a4f7911, [I@1cea4fdf) 0.012s passed
collapseIntervalTest[1]([Ljava.lang.String;@4e9ab294, [I@72a522f1, [I@2365facb, DEL, [I@65b9ebee, [I@7e2cebdf, [I@25c5fc41, [I@29fae990) 0.001s passed
collapseIntervalTest[2]([Ljava.lang.String;@1483ecad, [I@7118a1b9, [I@3ca9e72d, DEL, [I@4dcb8e8b, [I@46a6f51b, [I@7287811f, [I@1e490ed) 0s passed
collapseIntervalTest[3]([Ljava.lang.String;@61b5c8a3, [I@2f7432f3, [I@ab2ac08, DUP, [I@4d73b25b, [I@24c8b86, [I@c21c296, [I@13ecedf6) 0s passed
collapseIntervalTest[4]([Ljava.lang.String;@252bc7ec, [I@279c94ad, [I@53eb4ef5, DUP, [I@7b3b0896, [I@d4a4ba, [I@432e61f1, [I@4a3b0387) 0s passed
collapseIntervalTest[5]([Ljava.lang.String;@4c33450c, [I@7ca29492, [I@6e1787ba, BND, [I@39482f2b, [I@6f05062b, [I@76b195d, [I@5513745d) 0s passed
collapseIntervalTest[6]([Ljava.lang.String;@6a29476d, [I@35570a84, [I@7ba821ef, BND, [I@7cb8109, [I@2779acb2, [I@2af781f3, [I@106a6a1b) 0.001s passed
collapseIntervalTest[7]([Ljava.lang.String;@21845b36, [I@376aaeec, [I@749330a8, INS, [I@2caf182e, [I@2f71bb66, [I@4d8e6daa, [I@207512c3) 0s passed
collapseIntervalTest[8]([Ljava.lang.String;@56c72fff, [I@689afbb0, [I@60f10f6a, INS, [I@6c3600b7, [I@3e17219, [I@3c995eae, [I@54fb9c08) 0.001s passed
collapseInvalidAltAllelesTest 0s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@767785a4, INS, 100) 0s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@5634f627, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@721e5f57, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@5fb7b227, CTX, null) 0s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@12aa9370, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@41fc5625, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@61377842, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@26f29ee5, 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}]) 0s passed
collapseSampleGenotypesTest[14](sample, [[<INS>, <INS>], [N*, <INS>]], [{ECN=2, GQ=40}, {ECN=2, GQ=30}], N*, [sample <INS>/<INS> {ECN=2, GQ=40}]) 0.001s 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}]) 0s 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}]) 0.001s 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}]) 0s passed
collapseSampleGenotypesTest[2](sample, [[.], [.]], [{ECN=1}, {ECN=1}], N*, [sample . {ECN=1}]) 0.001s 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}]) 0s passed
collapseSampleGenotypesTest[33](sample, [[.], [.]], [{ECN=1, CN=1}, {ECN=1, CN=1}], N*, [sample . {CN=1, ECN=1}]) 0.001s 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}]) 0.001s 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}]) 0.001s 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}]) 0.001s passed
collapseSampleGenotypesTest[6](sample, [[N*, N*], [., .]], [{ECN=2}, {ECN=2}], N*, [sample N*/N* {ECN=2}]) 0s 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) 0.001s passed
collapseTypesTest[2]([INS], INS) 0s passed
collapseTypesTest[3]([INV], INV) 0s passed
collapseTypesTest[4]([BND], BND) 0s passed
collapseTypesTest[5]([CNV], CNV) 0s passed
collapseTypesTest[6]([DEL, DUP], CNV) 0.001s 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;@6b16aa6f, [[depth]], [depth1]) 0.001s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@2174fda1, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@2d99b35f, [[pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@7ee46aaf, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@5b4433dc, [[depth], [pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@3e42cff9, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@63a9ab7d, [[depth, pesr], [pesr]], [pesr1, mixed1]) 0s passed
makeBiallelicListTest[0](<DEL>, A*, 0, 0, []) 0s passed
makeBiallelicListTest[1](<DEL>, A*, 0, 1, [A*]) 0s 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>]) 0s 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*) 0.001s passed
testCollapse[0](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@524a96f5, org.broadinstitute.hellbender.tools.sv.SVCallRecord@72fb922c) 0.001s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@4dc74211, org.broadinstitute.hellbender.tools.sv.SVCallRecord@4bbc9862) 0.001s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@7fec198a, org.broadinstitute.hellbender.tools.sv.SVCallRecord@8cc1bac) 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) 0.001s passed
testGetDistance[0](5, 10, [I@62808e8d, [I@5c26ab0a, 15) 0s passed
testGetDistance[1](5, 10, [I@6ddd71cc, [I@b4f7e1c, 5) 0s passed
testGetDistance[2](5, 10, [I@6c720765, [I@6a275836, 10) 0s passed
testGetDistance[3](5, 10, [I@3f41a1f3, [I@4374c051, 0) 0s passed
testGetDistance[4](5, 10, [I@4a547f9d, [I@7828111d, 11) 0s passed
testGetDistance[5](0, 0, [I@184b8899, [I@718aa49a, 0) 0s passed
testGetDistance[6](-5, -10, [I@d6de944, [I@49a6b730, 11) 0s passed
testHarmonizeAltAlleles[0]([<DEL>], [[null A*/<DEL>]], null) 0s passed
testHarmonizeAltAlleles[1]([<DEL>], [[null A*/A*]], null) 0s 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>]]) 0s passed