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

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

tests
0

failures
0

ignored
0.057s

duration
100%

successful

Tests

Test Duration Result
collapseAlgorithmsTest[0]([[depth]], [depth]) 0.001s passed
collapseAlgorithmsTest[10]([[depth, pesr], [depth, pesr]], [depth, pesr]) 0s 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;@7bd6a7f9, [Ljava.lang.Integer;@690b6292, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@7fcbed77, [Ljava.lang.Integer;@2e2b1310, [<INS>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@22a7ff5d, [Ljava.lang.Integer;@5a362dc7, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@545ffe1, [Ljava.lang.Integer;@1805b503, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@4704b66a, [Ljava.lang.Integer;@70edffdb, [], []) 0s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@2b7e739, [Ljava.lang.Integer;@60e2b6e3, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@20f1c8ed, [Ljava.lang.Integer;@1dc26de5, [], []) 0.001s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@63f79099, [Ljava.lang.Integer;@4def8aaa, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@3ffa3cdb, [Ljava.lang.Integer;@605610e5, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@716cb4c0, [Ljava.lang.Integer;@1f9e42d2, [<DEL>], [<DEL>]) 0.001s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@759c0c14, [Ljava.lang.Integer;@61427cd3, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@3e4dabcb, [Ljava.lang.Integer;@2b24fcba, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@6c37b0de, [Ljava.lang.Integer;@3f774d60, [<INS:MEI>], [<INS:MEI>]) 0.001s passed
collapseAttributesTest[0]([Ljava.lang.String;@5331a22c, [Ljava.lang.Object;@79a1f55c, [Ljava.lang.String;@4c39eac6, [Ljava.lang.Object;@815e8e3, [Ljava.lang.String;@566b1b0f, [Ljava.lang.Object;@20961f8b, OR) 0s passed
collapseAttributesTest[10]([Ljava.lang.String;@6b5df313, [Ljava.lang.Object;@1a6aecec, [Ljava.lang.String;@51989b17, [Ljava.lang.Object;@12f52ca4, [Ljava.lang.String;@16b48082, [Ljava.lang.Object;@5bf41334, OR) 0s passed
collapseAttributesTest[11]([Ljava.lang.String;@750afe12, [Ljava.lang.Object;@4788c0a1, [Ljava.lang.String;@3c9e06d7, [Ljava.lang.Object;@79a1f0a1, [Ljava.lang.String;@5bf97be9, [Ljava.lang.Object;@5af535ff, OR) 0s passed
collapseAttributesTest[12]([Ljava.lang.String;@60c3f653, [Ljava.lang.Object;@7075ef91, [Ljava.lang.String;@35c66ad, [Ljava.lang.Object;@1c94d976, [Ljava.lang.String;@639ad5d9, [Ljava.lang.Object;@3ccca75c, AND) 0s passed
collapseAttributesTest[13]([Ljava.lang.String;@53a1cff1, [Ljava.lang.Object;@a8e649e, [Ljava.lang.String;@7802fc4e, [Ljava.lang.Object;@1994665d, [Ljava.lang.String;@4497fcd9, [Ljava.lang.Object;@3d44da41, AND) 0s passed
collapseAttributesTest[14]([Ljava.lang.String;@685783b1, [Ljava.lang.Object;@135ddb56, [Ljava.lang.String;@8508dae, [Ljava.lang.Object;@71d3776, [Ljava.lang.String;@5303762f, [Ljava.lang.Object;@2ef99072, AND) 0s passed
collapseAttributesTest[15]([Ljava.lang.String;@4c006046, [Ljava.lang.Object;@4fad5e7, [Ljava.lang.String;@6662af0a, [Ljava.lang.Object;@665f19d, [Ljava.lang.String;@4928a347, [Ljava.lang.Object;@1baf1268, AND) 0s passed
collapseAttributesTest[16]([Ljava.lang.String;@2e67df05, [Ljava.lang.Object;@71590f85, [Ljava.lang.String;@6565f3, [Ljava.lang.Object;@891f18f, [Ljava.lang.String;@189e986f, [Ljava.lang.Object;@218289de, AND) 0s passed
collapseAttributesTest[17]([Ljava.lang.String;@df9bfaa, [Ljava.lang.Object;@61c8139a, [Ljava.lang.String;@54b1ba04, [Ljava.lang.Object;@4796ae58, [Ljava.lang.String;@7d24def, [Ljava.lang.Object;@2627da4c, AND) 0s passed
collapseAttributesTest[18]([Ljava.lang.String;@d89b0d3, [Ljava.lang.Object;@18a129b8, [Ljava.lang.String;@cc655a, [Ljava.lang.Object;@67dc7d0, [Ljava.lang.String;@46b2e0e4, [Ljava.lang.Object;@574ffd63, AND) 0s passed
collapseAttributesTest[19]([Ljava.lang.String;@5ce1b67b, [Ljava.lang.Object;@d05d8c3, [Ljava.lang.String;@250988e5, [Ljava.lang.Object;@4481f9bd, [Ljava.lang.String;@1502cd38, [Ljava.lang.Object;@3662dc9b, ALWAYS_FALSE) 0s passed
collapseAttributesTest[1]([Ljava.lang.String;@48f08e9, [Ljava.lang.Object;@ab2d814, [Ljava.lang.String;@1a48e48e, [Ljava.lang.Object;@6c30efc4, [Ljava.lang.String;@10847aeb, [Ljava.lang.Object;@cea6297, OR) 0s passed
collapseAttributesTest[2]([Ljava.lang.String;@3afe1020, [Ljava.lang.Object;@91e76b6, [Ljava.lang.String;@563f53d8, [Ljava.lang.Object;@5bb1c104, [Ljava.lang.String;@1184b542, [Ljava.lang.Object;@6bd5ca02, OR) 0s passed
collapseAttributesTest[3]([Ljava.lang.String;@12b4a53d, [Ljava.lang.Object;@262e2c8c, [Ljava.lang.String;@636e6791, [Ljava.lang.Object;@631ff7a2, [Ljava.lang.String;@54353bb1, [Ljava.lang.Object;@3a837f7, OR) 0s passed
collapseAttributesTest[4]([Ljava.lang.String;@f54cdc4, [Ljava.lang.Object;@7241872c, [Ljava.lang.String;@3094111c, [Ljava.lang.Object;@776e4088, [Ljava.lang.String;@5e7d994c, [Ljava.lang.Object;@207b0d48, OR) 0s passed
collapseAttributesTest[5]([Ljava.lang.String;@3518882c, [Ljava.lang.Object;@71dc03a, [Ljava.lang.String;@7ff48cdc, [Ljava.lang.Object;@7029653c, [Ljava.lang.String;@181cafd, [Ljava.lang.Object;@68f4c6e7, OR) 0s passed
collapseAttributesTest[6]([Ljava.lang.String;@806a687, [Ljava.lang.Object;@7df5358, [Ljava.lang.String;@49d26eba, [Ljava.lang.Object;@139f1db4, [Ljava.lang.String;@2e90a3de, [Ljava.lang.Object;@532860c7, OR) 0s passed
collapseAttributesTest[7]([Ljava.lang.String;@62ccbd95, [Ljava.lang.Object;@49696c41, [Ljava.lang.String;@595713f3, [Ljava.lang.Object;@7bbd133c, [Ljava.lang.String;@7c9a39cb, [Ljava.lang.Object;@7e93497d, OR) 0s passed
collapseAttributesTest[8]([Ljava.lang.String;@c8dc1ef, [Ljava.lang.Object;@21f4f5d4, [Ljava.lang.String;@45488836, [Ljava.lang.Object;@a9339e5, [Ljava.lang.String;@687313e1, [Ljava.lang.Object;@6eaf016e, OR) 0.001s passed
collapseAttributesTest[9]([Ljava.lang.String;@7ce87db5, [Ljava.lang.Object;@c7485d2, [Ljava.lang.String;@1ac65143, [Ljava.lang.Object;@4cda8d3b, [Ljava.lang.String;@73e054c0, [Ljava.lang.Object;@5b12157b, OR) 0s passed
collapseIntervalRepresentativeByCoordinatesTest 0.002s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@192800d, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@52f9a620, false) 0.001s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2a882681, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@525b999, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@36af93ca, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5d7807b0, true) 0.001s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@42675041, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@81cba04, true) 0s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2c635953, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@547ef1c6, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@f64ce35, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@397ba74b, true) 0s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5e5d26e4, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@77614e7c, false) 0.001s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@78b906d, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@330a6b76, true) 0s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6f21c18f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@34723cfe, true) 0.001s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6c40ae2d, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@d0c3793, true) 0s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@61b06782, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@8e89c5f, false) 0s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@69c00140, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7cc7769d, false) 0s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2f3ba597, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4d555b85, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@34f636a5, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5d55eb7a, false) 0s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@79ae2d13, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7ce87f9d, false) 0s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@77ec911, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@55d3c0dd, false) 0s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@369773fd, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@47d0127f, false) 0s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2f8a82e9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@688e2e8d, true) 0s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@49fb77d0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@321d39cc, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3de473d9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2fb3c642, true) 0s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2b009051, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@35645453, true) 0.001s passed
collapseIntervalTest[0]([Ljava.lang.String;@41f4693a, [I@33116b8e, [I@54ff871a, DEL, [I@4c94621d, [I@2ecb7f0c, [I@16be2c40, [I@3e51beda) 0.012s passed
collapseIntervalTest[1]([Ljava.lang.String;@21e5feb, [I@33742179, [I@6ca1c156, DEL, [I@521f2a23, [I@228ed68c, [I@30e3544d, [I@522a9876) 0.002s passed
collapseIntervalTest[2]([Ljava.lang.String;@59e938a4, [I@323a47fe, [I@eb9b76c, DEL, [I@776eedad, [I@6752d7fc, [I@7b7695f, [I@4476ac12) 0s passed
collapseIntervalTest[3]([Ljava.lang.String;@3569f0f1, [I@9a88a92, [I@784fb189, DUP, [I@15c25cb6, [I@6fd6d887, [I@22e733f5, [I@27211dd9) 0.001s passed
collapseIntervalTest[4]([Ljava.lang.String;@794a3410, [I@62a9c857, [I@4dc9de0e, DUP, [I@6375af2a, [I@4b37ede0, [I@67f07fa1, [I@644ae4ff) 0s passed
collapseIntervalTest[5]([Ljava.lang.String;@5ea4abef, [I@3a4ddaed, [I@993bc47, BND, [I@632cfbc5, [I@18accf9c, [I@4ce2f4d6, [I@58070889) 0.001s passed
collapseIntervalTest[6]([Ljava.lang.String;@225fc6a2, [I@7940d27b, [I@19e3ce9a, BND, [I@4cd3e2f3, [I@10e5471d, [I@6fc98c70, [I@6859080d) 0s passed
collapseIntervalTest[7]([Ljava.lang.String;@1a9ce44, [I@2220780d, [I@2991524, INS, [I@4cc5c43b, [I@3d1f809, [I@2290186e, [I@686a192d) 0s passed
collapseIntervalTest[8]([Ljava.lang.String;@6f14ce3, [I@2400673b, [I@1c1bb1e7, INS, [I@71fa6aa7, [I@7d60a62f, [I@5a7e2f07, [I@1bab3926) 0s passed
collapseInvalidAltAllelesTest 0s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@6a225642, INS, 100) 0s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@27165978, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@6431ab21, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@484313a6, CTX, null) 0s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@763960eb, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@21dc1d99, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@467924d8, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@614da024, 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}]) 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}]) 0s passed
collapseSampleGenotypesTest[17](sample, [[N*, N*, <INS>], [N*, N*, N*]], [{ECN=3}, {ECN=3}], N*, [sample N*/N*/<INS> {ECN=3}]) 0.001s 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}]) 0s 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}]) 0.001s 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}]) 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}]) 0s 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}]) 0.001s 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}]) 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}]) 0.001s 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}]) 0.001s 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}]) 0s 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}]) 0.001s 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}]) 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) 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;@15c4b89b, [[depth]], [depth1]) 0.001s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@3eb814dd, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@5d852761, [[pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@12eb281f, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@c1765ad, [[depth], [pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@54d93fce, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@8c6a7db, [[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$OutputCluster@684138c5, org.broadinstitute.hellbender.tools.sv.SVCallRecord@6724f10e) 0s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@312cc16b, org.broadinstitute.hellbender.tools.sv.SVCallRecord@50ca509b) 0.001s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@5166f042, org.broadinstitute.hellbender.tools.sv.SVCallRecord@616549c) 0.003s passed
testComplexSubtypeAndIntervals 0.008s 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@6d8dc329, [I@52d1bb9c, 15) 0s passed
testGetDistance[1](5, 10, [I@7049d079, [I@735ed1d2, 5) 0s passed
testGetDistance[2](5, 10, [I@34ef9879, [I@a9b5c85, 10) 0s passed
testGetDistance[3](5, 10, [I@47c163bb, [I@f25176a, 0) 0s passed
testGetDistance[4](5, 10, [I@26df4e2f, [I@6a4f3df4, 11) 0s passed
testGetDistance[5](0, 0, [I@4298e4b4, [I@1e6a74fe, 0) 0s passed
testGetDistance[6](-5, -10, [I@77199818, [I@72216f0b, 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>]]) 0.001s passed