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

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

tests
0

failures
0

ignored
0.064s

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;@7daecd21, [Ljava.lang.Integer;@51ba8929, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@5ec80bbd, [Ljava.lang.Integer;@30f74965, [<INS>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@1cb58c8a, [Ljava.lang.Integer;@54a81a18, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@6803b02d, [Ljava.lang.Integer;@5862a07b, [<INS:MEI>], [<INS:MEI>]) 0.001s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@35b97c69, [Ljava.lang.Integer;@2c07277f, [], []) 0s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@470ce6e7, [Ljava.lang.Integer;@39a8905b, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@4e881e14, [Ljava.lang.Integer;@6e13e2fc, [], []) 0s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@3444ac8f, [Ljava.lang.Integer;@3ab26cad, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@7c5dbca5, [Ljava.lang.Integer;@6d6c4775, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@344d6bb3, [Ljava.lang.Integer;@2564410b, [<DEL>], [<DEL>]) 0.001s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@7ab5b01a, [Ljava.lang.Integer;@25fa5c0c, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@6f0969db, [Ljava.lang.Integer;@38eb2140, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@64514009, [Ljava.lang.Integer;@40b2aae9, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAttributesTest[0]([Ljava.lang.String;@64078e6a, [Ljava.lang.Object;@1170d81f, [Ljava.lang.String;@5c5cd332, [Ljava.lang.Object;@60232aad, [Ljava.lang.String;@380f9c1d, [Ljava.lang.Object;@2fa81b23, OR) 0.001s passed
collapseAttributesTest[10]([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
collapseAttributesTest[11]([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[12]([Ljava.lang.String;@2df019b8, [Ljava.lang.Object;@223ed38f, [Ljava.lang.String;@66ab765c, [Ljava.lang.Object;@319428ba, [Ljava.lang.String;@1c04dae9, [Ljava.lang.Object;@4872d04d, AND) 0.001s passed
collapseAttributesTest[13]([Ljava.lang.String;@5f7e2ca8, [Ljava.lang.Object;@1d07fb2, [Ljava.lang.String;@46f5030f, [Ljava.lang.Object;@18b77ec9, [Ljava.lang.String;@36821a1b, [Ljava.lang.Object;@34adce96, AND) 0s passed
collapseAttributesTest[14]([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[15]([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) 0.001s passed
collapseAttributesTest[16]([Ljava.lang.String;@7c5ae5c3, [Ljava.lang.Object;@36b5dbdf, [Ljava.lang.String;@3f35d13d, [Ljava.lang.Object;@482652f7, [Ljava.lang.String;@63f9c2cd, [Ljava.lang.Object;@7b0a864e, AND) 0s passed
collapseAttributesTest[17]([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[18]([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) 0.001s passed
collapseAttributesTest[19]([Ljava.lang.String;@c5dc3db, [Ljava.lang.Object;@2910c3ae, [Ljava.lang.String;@2182ebc7, [Ljava.lang.Object;@543895d2, [Ljava.lang.String;@3699c795, [Ljava.lang.Object;@193b6f5b, ALWAYS_FALSE) 0s passed
collapseAttributesTest[1]([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[2]([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) 0s passed
collapseAttributesTest[3]([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) 0.001s passed
collapseAttributesTest[4]([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[5]([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[6]([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) 0.001s passed
collapseAttributesTest[7]([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[8]([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[9]([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
collapseIntervalRepresentativeByCoordinatesTest 0.001s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3744c760, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7cb4fc46, false) 0s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2dfdea3a, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4b1339bf, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2cf073da, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6e1ef044, true) 0s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5b7b5484, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@743a9292, true) 0.001s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4691e2f5, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@47cf41d7, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@74691a1f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3d26c82d, true) 0s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@685e8e17, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@545bc8e1, false) 0.001s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1e23e1ef, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@79dcd7f1, true) 0s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@75abbb61, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@740610a2, true) 0s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6b351a54, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@43edd4e0, true) 0s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3dfef314, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7edab945, false) 0.001s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1181a376, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@ef09e1, false) 0s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6bbd645, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4c97e3d5, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@930b6f9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@15363eba, false) 0s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2258ca14, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2e5337d8, false) 0.001s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6a7eef27, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1ab6a093, false) 0s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7d2dfe9c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@60b721c9, false) 0s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1d9c18b9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@447cdbaa, true) 0.001s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6f67291f, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1243ad9a, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5479abd8, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2004f99, true) 0s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@39fbee74, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@20c5b5f8, true) 0.001s passed
collapseIntervalTest[0]([Ljava.lang.String;@5d6e77a4, [I@5bf9bb2, [I@76c5599b, DEL, [I@7231c423, [I@5c4c4e96, [I@25d73ca6, [I@7902b006) 0.012s passed
collapseIntervalTest[1]([Ljava.lang.String;@3c79be0f, [I@7aeb7bd6, [I@5c0bacaa, DEL, [I@7cb15360, [I@dc9033f, [I@2c5dfc9b, [I@2db27b46) 0.002s passed
collapseIntervalTest[2]([Ljava.lang.String;@b7b5e7, [I@2aa143ba, [I@7abe3d53, DEL, [I@372dc92e, [I@a885aa1, [I@2a9464d9, [I@21cb907d) 0s passed
collapseIntervalTest[3]([Ljava.lang.String;@3063493e, [I@39584147, [I@446d7669, DUP, [I@e1f17e6, [I@249f95a2, [I@5f36ba0f, [I@70c741be) 0s passed
collapseIntervalTest[4]([Ljava.lang.String;@5efb7f82, [I@34775090, [I@7e772d11, DUP, [I@76ad0058, [I@732f7660, [I@7d525b45, [I@3a0afe5b) 0s passed
collapseIntervalTest[5]([Ljava.lang.String;@2caf6813, [I@434896b0, [I@2e5d40a4, BND, [I@56aacc7b, [I@112d94d, [I@6e832c9, [I@42f40ad0) 0s passed
collapseIntervalTest[6]([Ljava.lang.String;@5572be5a, [I@124ba047, [I@700b9a54, BND, [I@5c658163, [I@1ca574db, [I@5323b690, [I@7fd65f9a) 0s passed
collapseIntervalTest[7]([Ljava.lang.String;@38fc1904, [I@7625bfbd, [I@3bc2146c, INS, [I@717c00f9, [I@299003eb, [I@72139933, [I@59d99269) 0.005s passed
collapseIntervalTest[8]([Ljava.lang.String;@6195e7d5, [I@f2120d5, [I@1afea182, INS, [I@4bcff08c, [I@52a1d6f, [I@38bb297, [I@6c96e1d5) 0s passed
collapseInvalidAltAllelesTest 0.001s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@53bc8c7e, INS, 100) 0.001s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@19bdfa3e, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@4f0b02a3, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@4ba056ab, CTX, null) 0s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@39da0e47, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@1c697ca0, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@43347199, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@6a49b3c7, CNV, 300) 0s passed
collapseSampleGenotypesTest[0](sample, [[]], [{ECN=0}], N*, [sample NA {ECN=0}]) 0s 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}]) 0s 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}]) 0.001s 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}]) 0.001s 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}]) 0.001s 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}]) 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) 0.001s 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) 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) 0.001s passed
collapseTypesTest[9]([INS, INS], INS) 0s passed
getMostPreciseCallsTest[0]([Ljava.lang.String;@62df1f0e, [[depth]], [depth1]) 0.001s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@605790e5, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@38300447, [[pesr]], [pesr1]) 0.001s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@32647dde, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@5c943847, [[depth], [pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@24305eca, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@2102eb7a, [[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*) 0s passed
testCollapse[0](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@77f43f3e, org.broadinstitute.hellbender.tools.sv.SVCallRecord@379ddab2) 0s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@67c64b9c, org.broadinstitute.hellbender.tools.sv.SVCallRecord@311d8595) 0s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@6f05d5f2, org.broadinstitute.hellbender.tools.sv.SVCallRecord@3acae925) 0.004s passed
testComplexSubtypeAndIntervals 0.006s 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) 0.002s passed
testConstructBndAllele[3](false, false, contigB, 20, G, [contigB:20[G) 0s passed
testGetDistance[0](5, 10, [I@7f913c47, [I@2c9573f1, 15) 0.001s passed
testGetDistance[1](5, 10, [I@3a1dc432, [I@4c18b432, 5) 0s passed
testGetDistance[2](5, 10, [I@bec2d81, [I@5f04449a, 10) 0s passed
testGetDistance[3](5, 10, [I@37a5ac85, [I@5d4f0fd5, 0) 0s passed
testGetDistance[4](5, 10, [I@504521ae, [I@4a9e6ea7, 11) 0s passed
testGetDistance[5](0, 0, [I@5aaecd25, [I@239fdf8f, 0) 0s passed
testGetDistance[6](-5, -10, [I@22f3b213, [I@e18848d, 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) 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>]]) 0.001s passed