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

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

tests
0

failures
0

ignored
0.062s

duration
100%

successful

Tests

Test Duration Result
collapseAlgorithmsTest[0]([[depth]], [depth]) 0s 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;@d4df4ce, [Ljava.lang.Integer;@470ce6e7, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@54a81a18, [Ljava.lang.Integer;@591e27f1, [<INS>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@1170d81f, [Ljava.lang.Integer;@5c5cd332, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@380f9c1d, [Ljava.lang.Integer;@2fa81b23, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@6e13e2fc, [Ljava.lang.Integer;@13448d2d, [], []) 0s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@3ab26cad, [Ljava.lang.Integer;@4b477d05, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@6d6c4775, [Ljava.lang.Integer;@44929971, [], []) 0.001s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@2564410b, [Ljava.lang.Integer;@2a3ced3d, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@25fa5c0c, [Ljava.lang.Integer;@22112da1, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@38eb2140, [Ljava.lang.Integer;@4f06006d, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@40b2aae9, [Ljava.lang.Integer;@2132629e, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@30f74965, [Ljava.lang.Integer;@65c75870, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@49588c70, [Ljava.lang.Integer;@43ee585f, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAttributesTest[0]([Ljava.lang.String;@6cd8aee2, [Ljava.lang.Object;@28f33810, [Ljava.lang.String;@476d5f2e, [Ljava.lang.Object;@6e56f5d4, [Ljava.lang.String;@4750e942, [Ljava.lang.Object;@76527a00, OR) 0s passed
collapseAttributesTest[10]([Ljava.lang.String;@2a0154f7, [Ljava.lang.Object;@237e61ac, [Ljava.lang.String;@19abe8f7, [Ljava.lang.Object;@6f36c42, [Ljava.lang.String;@26753687, [Ljava.lang.Object;@765650e4, OR) 0s passed
collapseAttributesTest[11]([Ljava.lang.String;@2df019b8, [Ljava.lang.Object;@223ed38f, [Ljava.lang.String;@66ab765c, [Ljava.lang.Object;@319428ba, [Ljava.lang.String;@1c04dae9, [Ljava.lang.Object;@4872d04d, OR) 0s passed
collapseAttributesTest[12]([Ljava.lang.String;@65977161, [Ljava.lang.Object;@5f7e2ca8, [Ljava.lang.String;@1d07fb2, [Ljava.lang.Object;@46f5030f, [Ljava.lang.String;@18b77ec9, [Ljava.lang.Object;@36821a1b, AND) 0s passed
collapseAttributesTest[13]([Ljava.lang.String;@794c22cd, [Ljava.lang.Object;@5fb8ad3d, [Ljava.lang.String;@5bb0122, [Ljava.lang.Object;@2d4eba14, [Ljava.lang.String;@358caf3a, [Ljava.lang.Object;@2fc72df3, AND) 0s passed
collapseAttributesTest[14]([Ljava.lang.String;@2aee0173, [Ljava.lang.Object;@7acb8e6b, [Ljava.lang.String;@6c758c74, [Ljava.lang.Object;@5a32ab89, [Ljava.lang.String;@8dcc25, [Ljava.lang.Object;@2693b289, AND) 0s passed
collapseAttributesTest[15]([Ljava.lang.String;@29e40db1, [Ljava.lang.Object;@47e6004c, [Ljava.lang.String;@7c5ae5c3, [Ljava.lang.Object;@36b5dbdf, [Ljava.lang.String;@3f35d13d, [Ljava.lang.Object;@482652f7, AND) 0.001s passed
collapseAttributesTest[16]([Ljava.lang.String;@106c4a72, [Ljava.lang.Object;@3d2e1d18, [Ljava.lang.String;@12b9d405, [Ljava.lang.Object;@402d443d, [Ljava.lang.String;@32e0b990, [Ljava.lang.Object;@7f6ba409, AND) 0s passed
collapseAttributesTest[17]([Ljava.lang.String;@988eae9, [Ljava.lang.Object;@3e93ee71, [Ljava.lang.String;@1cfa5e46, [Ljava.lang.Object;@4df5b562, [Ljava.lang.String;@3e4d197, [Ljava.lang.Object;@222557fc, AND) 0s passed
collapseAttributesTest[18]([Ljava.lang.String;@c5dc3db, [Ljava.lang.Object;@2910c3ae, [Ljava.lang.String;@2182ebc7, [Ljava.lang.Object;@543895d2, [Ljava.lang.String;@3699c795, [Ljava.lang.Object;@193b6f5b, AND) 0.001s passed
collapseAttributesTest[19]([Ljava.lang.String;@3fd7f545, [Ljava.lang.Object;@470a2845, [Ljava.lang.String;@589c648, [Ljava.lang.Object;@21e72fb2, [Ljava.lang.String;@219a9b16, [Ljava.lang.Object;@3744c760, ALWAYS_FALSE) 0s passed
collapseAttributesTest[1]([Ljava.lang.String;@2ca6937, [Ljava.lang.Object;@42908ad5, [Ljava.lang.String;@27777afd, [Ljava.lang.Object;@22e7ec5f, [Ljava.lang.String;@7335aae5, [Ljava.lang.Object;@35355074, OR) 0.001s passed
collapseAttributesTest[2]([Ljava.lang.String;@3411e0d7, [Ljava.lang.Object;@6a2d0632, [Ljava.lang.String;@75044df3, [Ljava.lang.Object;@17caf362, [Ljava.lang.String;@2c66be14, [Ljava.lang.Object;@2e78213c, OR) 0s passed
collapseAttributesTest[3]([Ljava.lang.String;@39d5376c, [Ljava.lang.Object;@20dab85c, [Ljava.lang.String;@4fc41cba, [Ljava.lang.Object;@120bb5b5, [Ljava.lang.String;@2f59ecf, [Ljava.lang.Object;@7798de95, OR) 0s passed
collapseAttributesTest[4]([Ljava.lang.String;@573f95b2, [Ljava.lang.Object;@79927a7c, [Ljava.lang.String;@484f7fad, [Ljava.lang.Object;@61d87509, [Ljava.lang.String;@4ae1ee85, [Ljava.lang.Object;@20ca2c3f, OR) 0s passed
collapseAttributesTest[5]([Ljava.lang.String;@3199c2c1, [Ljava.lang.Object;@74c997b1, [Ljava.lang.String;@593f6c3, [Ljava.lang.Object;@4afb2c90, [Ljava.lang.String;@358b70c4, [Ljava.lang.Object;@d471ddb, OR) 0s passed
collapseAttributesTest[6]([Ljava.lang.String;@474f69d, [Ljava.lang.Object;@6a17ab87, [Ljava.lang.String;@5f0bcadb, [Ljava.lang.Object;@e182453, [Ljava.lang.String;@2d7bfb13, [Ljava.lang.Object;@7ae736a8, OR) 0s passed
collapseAttributesTest[7]([Ljava.lang.String;@34ceefb5, [Ljava.lang.Object;@461f295c, [Ljava.lang.String;@50e0541, [Ljava.lang.Object;@25a41143, [Ljava.lang.String;@6654e105, [Ljava.lang.Object;@59be715a, OR) 0s passed
collapseAttributesTest[8]([Ljava.lang.String;@29c471f6, [Ljava.lang.Object;@6859f102, [Ljava.lang.String;@424769f2, [Ljava.lang.Object;@1467dcd0, [Ljava.lang.String;@1ea6446b, [Ljava.lang.Object;@39d0775c, OR) 0s passed
collapseAttributesTest[9]([Ljava.lang.String;@6a8a54f5, [Ljava.lang.Object;@4623c0d3, [Ljava.lang.String;@7c7335dc, [Ljava.lang.Object;@3095e9c6, [Ljava.lang.String;@8802edd, [Ljava.lang.Object;@50fd4246, OR) 0s passed
collapseIntervalRepresentativeByCoordinatesTest 0.001s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@15363eba, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6d6e8dfc, false) 0.001s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@743a9292, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6dbfd081, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@47cf41d7, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@67c1f5be, true) 0s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3d26c82d, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5af7a7, true) 0s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@545bc8e1, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5f3705e7, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@14b53f58, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1e23e1ef, true) 0s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@485902cd, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@75abbb61, false) 0s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@43edd4e0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@72a4f3f, true) 0s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7edab945, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@533d28aa, true) 0s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4c97e3d5, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@672c6b93, true) 0s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5bf9bb2, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@76c5599b, false) 0s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2e5337d8, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@ab40f46, false) 0s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5c4c4e96, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@25d73ca6, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7740028a, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@409a164d, false) 0.001s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1ab6a093, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6d95b51d, false) 0s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1d9c18b9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@447cdbaa, false) 0s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6f67291f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1243ad9a, false) 0s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2004f99, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@d200d3e, true) 0s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@20c5b5f8, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@20395afe, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4b1339bf, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@46f43f50, true) 0s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6e1ef044, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3c92f2f9, true) 0s passed
collapseIntervalTest[0]([Ljava.lang.String;@5ee63d9, [I@3b68a50c, [I@27c68ccb, DEL, [I@4ba88ab5, [I@3d2ec8b2, [I@43905ade, [I@502326b3) 0.012s passed
collapseIntervalTest[1]([Ljava.lang.String;@5bee07c3, [I@1e7b277a, [I@5d81b90a, DEL, [I@635791b7, [I@48ac4201, [I@f2bec99, [I@5f324d9f) 0.001s passed
collapseIntervalTest[2]([Ljava.lang.String;@78f649d3, [I@3063493e, [I@39584147, DEL, [I@446d7669, [I@e1f17e6, [I@249f95a2, [I@5f36ba0f) 0.001s passed
collapseIntervalTest[3]([Ljava.lang.String;@611d867, [I@5efb7f82, [I@34775090, DUP, [I@7e772d11, [I@76ad0058, [I@732f7660, [I@7d525b45) 0s passed
collapseIntervalTest[4]([Ljava.lang.String;@243b8682, [I@2caf6813, [I@434896b0, DUP, [I@2e5d40a4, [I@56aacc7b, [I@112d94d, [I@6e832c9) 0.001s passed
collapseIntervalTest[5]([Ljava.lang.String;@423ddfe1, [I@5572be5a, [I@124ba047, BND, [I@700b9a54, [I@5c658163, [I@1ca574db, [I@5323b690) 0s passed
collapseIntervalTest[6]([Ljava.lang.String;@f48a79a, [I@38fc1904, [I@7625bfbd, BND, [I@3bc2146c, [I@717c00f9, [I@299003eb, [I@72139933) 0.001s passed
collapseIntervalTest[7]([Ljava.lang.String;@48332a63, [I@6195e7d5, [I@f2120d5, INS, [I@1afea182, [I@4bcff08c, [I@52a1d6f, [I@38bb297) 0s passed
collapseIntervalTest[8]([Ljava.lang.String;@58e9375b, [I@d7d984c, [I@53bc8c7e, INS, [I@8ff4795, [I@19bdfa3e, [I@78e3bebd, [I@4f0b02a3) 0.001s passed
collapseInvalidAltAllelesTest 0s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@2e530f34, INS, 100) 0s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@55b56db3, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@2af5eab6, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@3d1254b9, CTX, null) 0.001s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@6f6c4462, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@20ac726c, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@a9e31e8, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@64bed8b2, 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}]) 0.001s 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}]) 0.001s 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}]) 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}]) 0.001s 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}]) 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}]) 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}]) 0.001s 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}]) 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}]) 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}]) 0.001s 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;@14484887, [[depth]], [depth1]) 0s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@5c943847, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@24305eca, [[pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@4ebf82d9, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@7952348f, [[depth], [pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@7d26b390, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@76b49d0, [[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>]) 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$OutputCluster@3acae925, org.broadinstitute.hellbender.tools.sv.SVCallRecord@67a6f2c4) 0.001s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@2a47fb5d, org.broadinstitute.hellbender.tools.sv.SVCallRecord@47a9bcf1) 0.001s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@1ca2d595, org.broadinstitute.hellbender.tools.sv.SVCallRecord@92a584f) 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@5f04449a, [I@5634c26c, 15) 0s passed
testGetDistance[1](5, 10, [I@5d4f0fd5, [I@2092b072, 5) 0s passed
testGetDistance[2](5, 10, [I@4a9e6ea7, [I@6f8af186, 10) 0s passed
testGetDistance[3](5, 10, [I@239fdf8f, [I@1acd660d, 0) 0s passed
testGetDistance[4](5, 10, [I@e18848d, [I@53a65166, 11) 0s passed
testGetDistance[5](0, 0, [I@1df6f57d, [I@578036a2, 0) 0.001s passed
testGetDistance[6](-5, -10, [I@41d1bcbd, [I@6ba6f4e7, 11) 0s passed
testHarmonizeAltAlleles[0]([<DEL>], [[null A*/<DEL>]], null) 0.001s 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) 0s 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