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

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

tests
0

failures
0

ignored
0.107s

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]) 0.001s passed
collapseAlgorithmsTest[8]([[pesrB, pesrA], [pesrA]], [pesrA, pesrB]) 0s passed
collapseAlgorithmsTest[9]([[pesr], [depth]], [depth, pesr]) 0s passed
collapseAltAllelesTest[0]([[]], DEL, [Ljava.lang.Integer;@511f21f9, [Ljava.lang.Integer;@5f97d43e, [], []) 0.001s passed
collapseAltAllelesTest[10]([[<INS>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@2a97b4b8, [Ljava.lang.Integer;@250fc0d1, [<INS>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[11]([[<INS:MEI>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@5ec10ab1, [Ljava.lang.Integer;@6701fbf3, [<INS:MEI>], [<INS:MEI:SVA>]) 0s passed
collapseAltAllelesTest[12]([[<INS:MEI:LINE>], [<INS:MEI:SVA>]], INS, [Ljava.lang.Integer;@2e962cec, [Ljava.lang.Integer;@78543f0d, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAltAllelesTest[1]([[N*]], DEL, [Ljava.lang.Integer;@5dcbdcb9, [Ljava.lang.Integer;@4dd31687, [], []) 0s passed
collapseAltAllelesTest[2]([[A*]], DEL, [Ljava.lang.Integer;@22d82fe8, [Ljava.lang.Integer;@2175111e, [], []) 0s passed
collapseAltAllelesTest[3]([[.]], DEL, [Ljava.lang.Integer;@35b5056e, [Ljava.lang.Integer;@56f1db5f, [], []) 0.001s passed
collapseAltAllelesTest[4]([[A]], INS, [Ljava.lang.Integer;@11e8e183, [Ljava.lang.Integer;@c6b08a5, [A], [A]) 0s passed
collapseAltAllelesTest[5]([[<DEL>]], DEL, [Ljava.lang.Integer;@25874884, [Ljava.lang.Integer;@7335414e, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[6]([[N*], [<DEL>]], DEL, [Ljava.lang.Integer;@33c976b1, [Ljava.lang.Integer;@2c95cb24, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[7]([[N*, N*], [N*, <DEL>]], DEL, [Ljava.lang.Integer;@28ec35e3, [Ljava.lang.Integer;@5068a2b1, [<DEL>], [<DEL>]) 0s passed
collapseAltAllelesTest[8]([[N*, <DUP>], [N*, <DEL>]], CNV, [Ljava.lang.Integer;@3938e876, [Ljava.lang.Integer;@70b2819f, [<DEL>, <DUP>], [<DEL>, <DUP>]) 0s passed
collapseAltAllelesTest[9]([[<INS:MEI>], [<INS:MEI>]], INS, [Ljava.lang.Integer;@3619ecd, [Ljava.lang.Integer;@7de4bd8f, [<INS:MEI>], [<INS:MEI>]) 0s passed
collapseAttributesTest[0]([Ljava.lang.String;@37d43b9b, [Ljava.lang.Object;@28ba90c1, [Ljava.lang.String;@71cf6e8c, [Ljava.lang.Object;@7545cb17, [Ljava.lang.String;@635b3ec7, [Ljava.lang.Object;@1f9b86f5, OR) 0s passed
collapseAttributesTest[10]([Ljava.lang.String;@19f72e12, [Ljava.lang.Object;@1ad4ff2a, [Ljava.lang.String;@625ae6d, [Ljava.lang.Object;@207bf6d8, [Ljava.lang.String;@5cdb7b, [Ljava.lang.Object;@3dcc59f5, OR) 0s passed
collapseAttributesTest[11]([Ljava.lang.String;@690337df, [Ljava.lang.Object;@f62ae87, [Ljava.lang.String;@50be5d6f, [Ljava.lang.Object;@48e0e779, [Ljava.lang.String;@38ad8c75, [Ljava.lang.Object;@22a10b71, OR) 0s passed
collapseAttributesTest[12]([Ljava.lang.String;@4fc28b23, [Ljava.lang.Object;@1b58788a, [Ljava.lang.String;@31881213, [Ljava.lang.Object;@2162e4a, [Ljava.lang.String;@595626b8, [Ljava.lang.Object;@1928930, AND) 0s passed
collapseAttributesTest[13]([Ljava.lang.String;@2ba7828b, [Ljava.lang.Object;@3e6945c6, [Ljava.lang.String;@16e6a643, [Ljava.lang.Object;@3514ea20, [Ljava.lang.String;@223095d3, [Ljava.lang.Object;@5683a326, AND) 0.001s passed
collapseAttributesTest[14]([Ljava.lang.String;@6723626f, [Ljava.lang.Object;@411bed55, [Ljava.lang.String;@a4aecc3, [Ljava.lang.Object;@59f59a0a, [Ljava.lang.String;@2539ab41, [Ljava.lang.Object;@3bd69bf6, AND) 0s passed
collapseAttributesTest[15]([Ljava.lang.String;@1377b7bf, [Ljava.lang.Object;@7bfc7533, [Ljava.lang.String;@74fa4891, [Ljava.lang.Object;@28245839, [Ljava.lang.String;@640c8cd, [Ljava.lang.Object;@1e0d70db, AND) 0s passed
collapseAttributesTest[16]([Ljava.lang.String;@4702faee, [Ljava.lang.Object;@576d4810, [Ljava.lang.String;@3609b8f2, [Ljava.lang.Object;@62dfe32e, [Ljava.lang.String;@32dab011, [Ljava.lang.Object;@fca4392, AND) 0s passed
collapseAttributesTest[17]([Ljava.lang.String;@6924ff83, [Ljava.lang.Object;@e19908e, [Ljava.lang.String;@5312940c, [Ljava.lang.Object;@5ac168e3, [Ljava.lang.String;@14574cdf, [Ljava.lang.Object;@5608233b, AND) 0s passed
collapseAttributesTest[18]([Ljava.lang.String;@40aa9bae, [Ljava.lang.Object;@6eb506d0, [Ljava.lang.String;@79b3f1c6, [Ljava.lang.Object;@3cc148d, [Ljava.lang.String;@172f88b1, [Ljava.lang.Object;@51ea9f02, AND) 0s passed
collapseAttributesTest[19]([Ljava.lang.String;@54ba7b3f, [Ljava.lang.Object;@3f3b0b19, [Ljava.lang.String;@3aac9173, [Ljava.lang.Object;@6e847a7, [Ljava.lang.String;@18cb7c6, [Ljava.lang.Object;@6608072d, ALWAYS_FALSE) 0s passed
collapseAttributesTest[1]([Ljava.lang.String;@4e6c4c55, [Ljava.lang.Object;@74fbee59, [Ljava.lang.String;@3794621d, [Ljava.lang.Object;@737e4a7b, [Ljava.lang.String;@5f5caea5, [Ljava.lang.Object;@747e0a31, OR) 0.001s passed
collapseAttributesTest[2]([Ljava.lang.String;@6142b9dd, [Ljava.lang.Object;@5bd11ad6, [Ljava.lang.String;@5ffaac1f, [Ljava.lang.Object;@4f55da9b, [Ljava.lang.String;@3bad0efd, [Ljava.lang.Object;@68f9a4f4, OR) 0s passed
collapseAttributesTest[3]([Ljava.lang.String;@309e874, [Ljava.lang.Object;@5080c40e, [Ljava.lang.String;@75fb04ee, [Ljava.lang.Object;@5c863996, [Ljava.lang.String;@1000303a, [Ljava.lang.Object;@46763680, OR) 0s passed
collapseAttributesTest[4]([Ljava.lang.String;@62048ab, [Ljava.lang.Object;@173039b5, [Ljava.lang.String;@6005cfe5, [Ljava.lang.Object;@37635407, [Ljava.lang.String;@33822750, [Ljava.lang.Object;@25e95d04, OR) 0s passed
collapseAttributesTest[5]([Ljava.lang.String;@46b376bb, [Ljava.lang.Object;@64a9719a, [Ljava.lang.String;@bc70176, [Ljava.lang.Object;@eba64a9, [Ljava.lang.String;@53e1cd6b, [Ljava.lang.Object;@7ceb432c, OR) 0s passed
collapseAttributesTest[6]([Ljava.lang.String;@12568b11, [Ljava.lang.Object;@4f8186a5, [Ljava.lang.String;@69554e5a, [Ljava.lang.Object;@7244d87, [Ljava.lang.String;@210c4071, [Ljava.lang.Object;@627b5e5b, OR) 0s passed
collapseAttributesTest[7]([Ljava.lang.String;@472d201, [Ljava.lang.Object;@473e0536, [Ljava.lang.String;@7f8f120c, [Ljava.lang.Object;@2110b756, [Ljava.lang.String;@33e09baf, [Ljava.lang.Object;@4c02f50, OR) 0.001s passed
collapseAttributesTest[8]([Ljava.lang.String;@27d6ff8c, [Ljava.lang.Object;@105c253a, [Ljava.lang.String;@156322ce, [Ljava.lang.Object;@546f0f36, [Ljava.lang.String;@44d5a0a8, [Ljava.lang.Object;@35d128fd, OR) 0s passed
collapseAttributesTest[9]([Ljava.lang.String;@1512a767, [Ljava.lang.Object;@7c2b858d, [Ljava.lang.String;@4001dc35, [Ljava.lang.Object;@399ef33f, [Ljava.lang.String;@39b752f4, [Ljava.lang.Object;@1990afa2, OR) 0s passed
collapseIntervalRepresentativeByCoordinatesTest 0.001s passed
collapseIntervalRepresentativeTest[0](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5e9c6d8a, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6b760eb7, false) 0s passed
collapseIntervalRepresentativeTest[10](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@a8dedda, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6e089bcb, true) 0s passed
collapseIntervalRepresentativeTest[11](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@318ff889, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5409305f, true) 0.001s passed
collapseIntervalRepresentativeTest[12](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@51a6af38, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1f234e35, true) 0s passed
collapseIntervalRepresentativeTest[13](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@55691a59, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3152a0a3, true) 0s passed
collapseIntervalRepresentativeTest[14](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1e686da2, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3ce17e4, true) 0.001s passed
collapseIntervalRepresentativeTest[15](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@3b3639f9, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@66ee4640, false) 0s passed
collapseIntervalRepresentativeTest[16](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@43e6bcfd, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@361d56a3, true) 0.001s passed
collapseIntervalRepresentativeTest[17](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2461b519, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@5216e43c, true) 0s passed
collapseIntervalRepresentativeTest[18](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@411c5fa2, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@68fce3e5, true) 0.003s passed
collapseIntervalRepresentativeTest[19](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@13967a64, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@30d4d6fb, false) 0.001s passed
collapseIntervalRepresentativeTest[1](0.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@42d8b670, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7f15639c, false) 0.001s passed
collapseIntervalRepresentativeTest[20](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4483e237, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6466e599, false) 0s passed
collapseIntervalRepresentativeTest[2](null, 0.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@4101d2c7, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@466d87a1, false) 0s passed
collapseIntervalRepresentativeTest[3](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@58fcb07b, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@1724c649, false) 0.001s passed
collapseIntervalRepresentativeTest[4](-99.0, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@6e7d874c, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7d6f31ef, false) 0.002s passed
collapseIntervalRepresentativeTest[5](null, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@70916715, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@72d4d9ac, false) 0s passed
collapseIntervalRepresentativeTest[6](-99.0, null, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@66d8a602, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@32950acc, true) 0s passed
collapseIntervalRepresentativeTest[7](null, -99.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@cf822a6, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2fb36d8d, false) 0s passed
collapseIntervalRepresentativeTest[8](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@639f5460, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@2e3fa7a7, true) 0.004s passed
collapseIntervalRepresentativeTest[9](-10.0, -9.0, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@7953a656, [Lorg.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants$EvidenceTypes;@60f6c148, true) 0s passed
collapseIntervalTest[0]([Ljava.lang.String;@a15e4fd, [I@515c3dd2, [I@245504d, DEL, [I@6c9fe061, [I@4988c303, [I@798ac54d, [I@51653509) 0.021s passed
collapseIntervalTest[1]([Ljava.lang.String;@49588c70, [I@43ee585f, [I@1cb58c8a, DEL, [I@54a81a18, [I@591e27f1, [I@6803b02d, [I@5862a07b) 0.002s passed
collapseIntervalTest[2]([Ljava.lang.String;@155788a7, [I@6cd8aee2, [I@28f33810, DEL, [I@476d5f2e, [I@6e56f5d4, [I@4750e942, [I@76527a00) 0s passed
collapseIntervalTest[3]([Ljava.lang.String;@2ca6937, [I@42908ad5, [I@27777afd, DUP, [I@22e7ec5f, [I@7335aae5, [I@35355074, [I@290964bd) 0.001s passed
collapseIntervalTest[4]([Ljava.lang.String;@6a2d0632, [I@75044df3, [I@17caf362, DUP, [I@2c66be14, [I@2e78213c, [I@79c48ad5, [I@39d5376c) 0.002s passed
collapseIntervalTest[5]([Ljava.lang.String;@4fc41cba, [I@120bb5b5, [I@2f59ecf, BND, [I@7798de95, [I@18563d10, [I@573f95b2, [I@79927a7c) 0s passed
collapseIntervalTest[6]([Ljava.lang.String;@61d87509, [I@4ae1ee85, [I@20ca2c3f, BND, [I@134b9d9c, [I@3199c2c1, [I@74c997b1, [I@593f6c3) 0s passed
collapseIntervalTest[7]([Ljava.lang.String;@358b70c4, [I@d471ddb, [I@17f8c75e, INS, [I@474f69d, [I@6a17ab87, [I@5f0bcadb, [I@e182453) 0s passed
collapseIntervalTest[8]([Ljava.lang.String;@7ae736a8, [I@7b3b763d, [I@34ceefb5, INS, [I@461f295c, [I@50e0541, [I@25a41143, [I@6654e105) 0s passed
collapseInvalidAltAllelesTest 0s passed
collapseLengthTest[0](org.broadinstitute.hellbender.tools.sv.SVCallRecord@29c471f6, INS, 100) 0s passed
collapseLengthTest[1](org.broadinstitute.hellbender.tools.sv.SVCallRecord@424769f2, INS, null) 0s passed
collapseLengthTest[2](org.broadinstitute.hellbender.tools.sv.SVCallRecord@1ea6446b, BND, null) 0s passed
collapseLengthTest[3](org.broadinstitute.hellbender.tools.sv.SVCallRecord@40a1916d, CTX, null) 0s passed
collapseLengthTest[4](org.broadinstitute.hellbender.tools.sv.SVCallRecord@4623c0d3, CPX, 50) 0s passed
collapseLengthTest[5](org.broadinstitute.hellbender.tools.sv.SVCallRecord@3095e9c6, DEL, 100) 0s passed
collapseLengthTest[6](org.broadinstitute.hellbender.tools.sv.SVCallRecord@50fd4246, DUP, 200) 0s passed
collapseLengthTest[7](org.broadinstitute.hellbender.tools.sv.SVCallRecord@2a0154f7, 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}]) 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}]) 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}]) 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}]) 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}]) 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}]) 0.001s passed
collapseSampleGenotypesTest[27](sample, [[N*, N*], [N*, <DUP>]], [{ECN=2, CN=2}, {ECN=2, CN=3}], N*, [sample N*/<DUP> {CN=3, ECN=2}]) 0s passed
collapseSampleGenotypesTest[28](sample, [[N*, N*], [<DUP>, <DUP>]], [{ECN=2, CN=2}, {ECN=2, CN=4}], N*, [sample <DUP>/<DUP> {CN=4, ECN=2}]) 0s passed
collapseSampleGenotypesTest[29](sample, [[N*, N*], [N*, N*]], [{ECN=2, CN=2}, {ECN=2, CN=2}], N*, [sample N*/N* {CN=2, ECN=2}]) 0.001s passed
collapseSampleGenotypesTest[2](sample, [[.], [.]], [{ECN=1}, {ECN=1}], N*, [sample . {ECN=1}]) 0s passed
collapseSampleGenotypesTest[30](sample, [[N*, N*, N*], [N*, N*, <DUP>]], [{ECN=3, CN=3}, {ECN=3, CN=4}], N*, [sample N*/N*/<DUP> {CN=4, ECN=3}]) 0s passed
collapseSampleGenotypesTest[31](sample, [[N*, N*, N*], [N*, <DUP>, <DUP>]], [{ECN=3, CN=3}, {ECN=3, CN=5}], N*, [sample N*/<DUP>/<DUP> {CN=5, ECN=3}]) 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}]) 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}]) 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}]) 0.001s 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}]) 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}]) 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}]) 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}]) 0.001s 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}]) 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}]) 0.001s 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) 0s passed
collapseTypesTest[9]([INS, INS], INS) 0s passed
getMostPreciseCallsTest[0]([Ljava.lang.String;@470a2845, [[depth]], [depth1]) 0s passed
getMostPreciseCallsTest[1]([Ljava.lang.String;@3744c760, [[depth], [depth]], [depth1, depth2]) 0s passed
getMostPreciseCallsTest[2]([Ljava.lang.String;@64b6d6dd, [[pesr]], [pesr1]) 0s passed
getMostPreciseCallsTest[3]([Ljava.lang.String;@5b628376, [[pesr], [pesr]], [pesr1, pesr2]) 0s passed
getMostPreciseCallsTest[4]([Ljava.lang.String;@15363eba, [[depth], [pesr]], [pesr1]) 0.003s passed
getMostPreciseCallsTest[5]([Ljava.lang.String;@2258ca14, [[depth, pesr], [depth]], [mixed1]) 0s passed
getMostPreciseCallsTest[6]([Ljava.lang.String;@ab40f46, [[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>]) 0.001s 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$OutputCluster@1d9c18b9, org.broadinstitute.hellbender.tools.sv.SVCallRecord@447cdbaa) 0.003s passed
testCollapse[1](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@6f67291f, org.broadinstitute.hellbender.tools.sv.SVCallRecord@1243ad9a) 0.001s passed
testCollapse[2](org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine$OutputCluster@5479abd8, org.broadinstitute.hellbender.tools.sv.SVCallRecord@2004f99) 0.010s passed
testComplexSubtypeAndIntervals 0.020s passed
testConstructBndAllele[0](true, true, contigB, 10, A, A]contigB:10]) 0.001s passed
testConstructBndAllele[1](true, false, contigB, 10, T, T[contigB:10[) 0s passed
testConstructBndAllele[2](false, true, contigB, 20, C, ]contigB:20]C) 0.005s passed
testConstructBndAllele[3](false, false, contigB, 20, G, [contigB:20[G) 0s passed
testGetDistance[0](5, 10, [I@25d73ca6, [I@7902b006, 15) 0.001s passed
testGetDistance[1](5, 10, [I@3b68a50c, [I@27c68ccb, 5) 0s passed
testGetDistance[2](5, 10, [I@3d2ec8b2, [I@43905ade, 10) 0s passed
testGetDistance[3](5, 10, [I@5f51f320, [I@14f1db20, 0) 0s passed
testGetDistance[4](5, 10, [I@1c298769, [I@4cb1af3f, 11) 0s passed
testGetDistance[5](0, 0, [I@32bff23d, [I@627d29cc, 0) 0s passed
testGetDistance[6](-5, -10, [I@6f914212, [I@22726bc7, 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) 0.001s 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