| Test |
Duration |
Result |
| testConfigurationSorting[0]([AssemblyContigWithFineTunedAlignments{sourceTig=(asm001160:tig00000, [1_1317_chr1:93876139-93877455_-_1317M516S_60_0_1317_O, 1318_1833_chrUn_JTFH01001621v1_decoy:641-1154_-_1317H408M2I106M_60_5_481_O, 1661_1727_chr10:96642377-96642443_+_1660H67M106H_60_5_42_O]), insertionMappings=[1428_1492_chr15:43085606-43085670_+_1427H65M341H_0_2_55_O, 1595_1668_chr1:61662787-61662860_-_1594H74M165H_12_2_64_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}, AssemblyContigWithFineTunedAlignments{sourceTig=(asm001160:tig00000, [1_1317_chr1:93876139-93877455_-_1317M516S_60_0_1317_O, 1318_1833_chrUn_JTFH01001621v1_decoy:641-1154_-_1317H408M2I106M_60_5_481_O]), insertionMappings=[1428_1492_chr15:43085606-43085670_+_1427H65M341H_0_2_55_O, 1595_1668_chr1:61662787-61662860_-_1594H74M165H_12_2_64_O, 1661_1727_chr10:96642377-96642443_+_1660H67M106H_60_5_42_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}], [AssemblyContigWithFineTunedAlignments{sourceTig=(asm001160:tig00000, [1_1317_chr1:93876139-93877455_-_1317M516S_60_0_1317_O, 1318_1833_chrUn_JTFH01001621v1_decoy:641-1154_-_1317H408M2I106M_60_5_481_O]), insertionMappings=[1428_1492_chr15:43085606-43085670_+_1427H65M341H_0_2_55_O, 1595_1668_chr1:61662787-61662860_-_1594H74M165H_12_2_64_O, 1661_1727_chr10:96642377-96642443_+_1660H67M106H_60_5_42_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}, AssemblyContigWithFineTunedAlignments{sourceTig=(asm001160:tig00000, [1_1317_chr1:93876139-93877455_-_1317M516S_60_0_1317_O, 1318_1833_chrUn_JTFH01001621v1_decoy:641-1154_-_1317H408M2I106M_60_5_481_O, 1661_1727_chr10:96642377-96642443_+_1660H67M106H_60_5_42_O]), insertionMappings=[1428_1492_chr15:43085606-43085670_+_1427H65M341H_0_2_55_O, 1595_1668_chr1:61662787-61662860_-_1594H74M165H_12_2_64_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}]) |
0s |
passed |
| testConfigurationSorting[1]([AssemblyContigWithFineTunedAlignments{sourceTig=(asm000168:tig00027, [1_66_chr1:4939436-4939501_+_66M223H_23_3_51_O, 55_193_chr1:4939534-4939672_+_54S139M96S_60_8_99_O, 156_289_chr1:4939535-4939668_+_155H134M_60_15_61_O]), insertionMappings=[137_289_chrUn_JTFH01000538v1_decoy:1338-1490_-_136H153M_60_1_148_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}, AssemblyContigWithFineTunedAlignments{sourceTig=(asm000168:tig00027, [1_66_chr1:4939436-4939501_+_66M223H_23_3_51_O, 55_193_chr1:4939534-4939672_+_54S139M96S_60_8_99_O, 137_289_chrUn_JTFH01000538v1_decoy:1338-1490_-_136H153M_60_1_148_O]), insertionMappings=[156_289_chr1:4939535-4939668_+_155H134M_60_15_61_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}], [AssemblyContigWithFineTunedAlignments{sourceTig=(asm000168:tig00027, [1_66_chr1:4939436-4939501_+_66M223H_23_3_51_O, 55_193_chr1:4939534-4939672_+_54S139M96S_60_8_99_O, 137_289_chrUn_JTFH01000538v1_decoy:1338-1490_-_136H153M_60_1_148_O]), insertionMappings=[156_289_chr1:4939535-4939668_+_155H134M_60_15_61_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}, AssemblyContigWithFineTunedAlignments{sourceTig=(asm000168:tig00027, [1_66_chr1:4939436-4939501_+_66M223H_23_3_51_O, 55_193_chr1:4939534-4939672_+_54S139M96S_60_8_99_O, 156_289_chr1:4939535-4939668_+_155H134M_60_15_61_O]), insertionMappings=[137_289_chrUn_JTFH01000538v1_decoy:1338-1490_-_136H153M_60_1_148_O], hasEquallyGoodAlnConfigurations=true, saTAGForGoodMappingToNonCanonicalChromosome='NONE'}]) |
0.001s |
passed |
| testFilterSecondaryConfigurationsByMappingQualityThreshold[0]([GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100123,+,222S78M,60,0,78], badMappings=[chr21,100123,+,222S78M,60,0,78]}, GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100099,+,98S24M78S,10,3,241, chr21,100123,+,222S78M,60,0,78], badMappings=[]}], 0, [GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100123,+,222S78M,60,0,78], badMappings=[chr21,100123,+,222S78M,60,0,78]}, GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100099,+,98S24M78S,10,3,241, chr21,100123,+,222S78M,60,0,78], badMappings=[]}]) |
0.001s |
passed |
| testFilterSecondaryConfigurationsByMappingQualityThreshold[1]([GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100123,+,222S78M,60,0,78], badMappings=[chr21,100123,+,222S78M,60,0,78]}, GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100099,+,98S24M78S,10,3,241, chr21,100123,+,222S78M,60,0,78], badMappings=[]}], 10, [GoodAndBadMappings{goodMappings=[chr21,100001,+,100M220S,60,0,100, chr21,100123,+,222S78M,60,0,78], badMappings=[chr21,100123,+,222S78M,60,0,78]}]) |
0s |
passed |
| testFilterSecondaryConfigurationsByMappingQualityThreshold[2]([GoodAndBadMappings{goodMappings=[chrUn_KN707896v1_decoy,6436,-,517S88M,60,3, chrUn_KI270519v1,137524,+,101S37M467S,3,1, chr5,49659827,-,332S112M161S,60,5,87, chr4,49639434,+,331S37M237S,60,1, chr10,41903518,+,372S74M159S,48,7], badMappings=[chr20,31162579,+,37S59M509S,0,5, chrUn_KN707896v1_decoy,6014,-,81M15I253M5D189M67S,0,34, chr20,31188805,+,298S43M264S,0,2, chr22_KI270736v1_random,101512,+,455S56M94S,0,1]}, GoodAndBadMappings{goodMappings=[chrUn_KN707896v1_decoy,6436,-,517S88M,60,3, chrUn_KI270519v1,137524,+,101S37M467S,3,1, chr5,49659827,-,332S112M161S,60,5,87, chr4,49639434,+,331S37M237S,60,1, chr10,41903518,+,372S74M159S,48,7, chr22_KI270736v1_random,101512,+,455S56M94S,0,1], badMappings=[chr20,31162579,+,37S59M509S,0,5, chrUn_KN707896v1_decoy,6014,-,81M15I253M5D189M67S,0,34, chr20,31188805,+,298S43M264S,0,2]}], 0, [GoodAndBadMappings{goodMappings=[chrUn_KN707896v1_decoy,6436,-,517S88M,60,3, chrUn_KI270519v1,137524,+,101S37M467S,3,1, chr5,49659827,-,332S112M161S,60,5,87, chr4,49639434,+,331S37M237S,60,1, chr10,41903518,+,372S74M159S,48,7], badMappings=[chr20,31162579,+,37S59M509S,0,5, chrUn_KN707896v1_decoy,6014,-,81M15I253M5D189M67S,0,34, chr20,31188805,+,298S43M264S,0,2, chr22_KI270736v1_random,101512,+,455S56M94S,0,1]}]) |
0s |
passed |
| testGetBetterNonCanonicalMapping[0]([chr21,2655749,-,125S394M,1,42,184, chr21,2667827,-,66M453H,0,3,51, chr21,2761512,-,95H50M374H,0,3,35, chr1_KI270762v1_alt,207249,-,38H252M229H,2,15,177, chr1_KI270762v1_alt,207251,-,66M453H,0,2,56], 184, null) |
0s |
passed |
| testGetBetterNonCanonicalMapping[1]([chr21,1422222,-,75M56I139M,60,56,142, chr2_KI270774v1_alt,105288,-,114M1I27M1I127M,56,13,179], 142, chr2_KI270774v1_alt,105288,-,114M1I27M1I127M,56,13,179) |
0s |
passed |
| testGetBetterNonCanonicalMapping[2]([chr20,188506254,-,182S253M,60,6,223, chr20,188507694,-,229M206H,60,22,119, chr4_KI270789v1_alt,167965,-,122M60I253M,60,62,289], 223, chr4_KI270789v1_alt,167965,-,122M60I253M,60,62,289) |
0s |
passed |
| testGetBetterNonCanonicalMapping[3]([chr1,933803,+,317M302H,60,7,282, chr1,934806,+,163S456M,60,8,416], 416, null) |
0s |
passed |
| testGetBetterNonCanonicalMapping[4]([chrUn_JTFH01001739v1_decoy,939,-,354M2D1883M86I1058M2I67M,60,98, chr14,16092705,-,3313S116M21S,9,8, chr8,43241450,+,369S34M2I84M2I183M3D25M1I126M2624S,6,62, chr8,43237624,-,2342S63M2I86M2I104M851S,0,24, chr14,16093049,-,2278S41M2I72M1057S,9,10, chr14,16093049,-,2194S113M1143S,9,9, chr22,11213752,+,1353S90M2007S,9,7, chr22,11212173,+,1435S209M1I125M2I43M2I45M1588S,9,46,164, chr8,43239662,+,2025S52M2I173M1198S,6,19, chr22,11212247,+,2329S134M1I299M687S,9,53, chr22,11213337,+,2708S134M608S,9,12, chr14,16095303,-,540S52M2858S,9,0, chrUn_KI270467v1,2467,+,3245S73M132S,9,5, chr4,49711819,-,14S102M3334S,9,7], 164, null) |
0s |
passed |
| testGetMaxOverlapPairs[0]([chr18,77371711,+,1447M1164S,60, chr18,77373176,+,1165H338M1108S,60, chr18,77373208,+,1447S184M980S,60, chr18,77373514,+,1165H388S1058M,60], {chr18,77373176,+,1165H338M1108S,60=(282,56), chr18,77371711,+,1447M1164S,60=(-1,282), chr18,77373514,+,1165H388S1058M,60=(78,-1), chr18,77373208,+,1447S184M980S,60=(56,78)}) |
0s |
passed |
| testHeuristicSpeedUpWhenFacingManyMappings |
0s |
passed |
| testMiscFunctions[0]((asm000063:tig00003, [1_787_chr21:1948156-1948936_+_257M4I182M2I342M361S_60_8_733_O, 893_1148_chr21:1948935-1949190_+_892H256M_60_3_241_O]), [chr21,1948156,+,257M4I182M2I342M361S,60,8,733], [chr21,1948156,+,257M4I182M2I342M361S,60,8,733, chr21,1948935,+,892H256M,60,3,241], 1, 2) |
0s |
passed |
| testMiscFunctions[1]((asm002608:tig00001, [1_270_chr2:1422222-1422435_-_75M56I139M_60_56_142_O, 1_270_chr2_KI270774v1_alt:105288-105555_-_114M1I27M1I127M_56_13_179_O]), [chr2_KI270774v1_alt,105288,-,127M1I27M1I114M,56,13,179], [chr2,1422222,-,139M56I75M,60,56,142], 3, 1) |
0s |
passed |
| testMiscFunctions[2]((asm027070:tig00000, [1_1002_chr1_KI270760v1_alt:22529-23531_+_966M1D36M2362H_14_3_975_O, 1_1002_chr21:30374719-30375721_+_966M1D36M2362H_60_6_960_O, 826_3364_chr1_KI270760v1_alt:23681-26220_+_825H33M1D2506M_60_2_2517_O, 826_3364_chr21:30375922-30378473_+_825S33M1D1047M7D553M5D906M_60_24_2423_O]), [chr21,30374719,+,966M1D36M2362H,60,6,960, chr1_KI270760v1_alt,23681,+,825H33M1D2506M,60,2,2517], [chr1_KI270760v1_alt,22529,+,966M1D36M2362H,14,3,975, chr1_KI270760v1_alt,23681,+,825H33M1D2506M,60,2,2517], 2, 2) |
0.001s |
passed |
| testMiscFunctions[3]((asm005003:tig00056, [1_682_chr20:60230348-60231029_-_682M_57_68_342_O, 1_627_chrUn_JTFH01001804v1_decoy:3674-4300_+_627M55H_60_1_622_O]), [chr20,60230348,-,682M,57,68,342, chrUn_JTFH01001804v1_decoy,3674,+,627M55H,60,1,622], [chr20,60230348,-,682M,57,68,342], 2, 1) |
0s |
passed |
| testNotDiscardForBadMQ[0]((unmapped, []), false) |
0s |
passed |
| testNotDiscardForBadMQ[1]((badMap, [1_151_chr1:1000000-1000150_+_151M_5_39_100_O]), false) |
0s |
passed |
| testNotDiscardForBadMQ[2]((lonelyGood, [1_100_chr21:100001-100100_+_100M220S_60_0_100_O, 99_122_chr21:100099-100122_+_98S24M78S_10_3_241_O]), false) |
0s |
passed |
| testNotDiscardForBadMQ[3]((asm000576:tig00001, [1_999_chr1:30894493-30895558_-_873M67D126M106S_60_70_901_O, 999_1105_chr2:32916450-32916556_-_998S107M_0_2_-1_O]), true) |
0s |
passed |
| testNotDiscardForBadMQ[4]((asm022620:tig00006, [1_1022_chr1:176967755-176968776_+_1022M_60_1_1017_O]), true) |
0.001s |
passed |
| testNotDiscardForBadMQ[5]((asm017085:tig00001, [1_145_chr10:91873437-91873581_+_145M147S_60_0_-1_O, 143_292_chr10:91874806-91874955_+_142S150M_60_0_150_O]), true) |
0s |
passed |
| testRemoveNonUniqueMappings[0](GoodAndBadMappings{goodMappings=[chrUn_JTFH01001925v1_decoy,600,+,646M4D370M,60,966,259], badMappings=[]}, GoodAndBadMappings{goodMappings=[chrUn_JTFH01001925v1_decoy,600,+,646M4D370M,60,966,259], badMappings=[]}, 20, 10) |
0s |
passed |
| testRemoveNonUniqueMappings[1](GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr1,137,+,130S64M,60,0,64], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr1,137,+,130S64M,60,0,64], badMappings=[]}, 20, 10) |
0s |
passed |
| testRemoveNonUniqueMappings[2](GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S29M101S,19,2,20, chr1,137,+,130S64M,60,0,64], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr1,137,+,130S64M,60,0,64], badMappings=[chr2,1,-,64S29M101S,19,2,20]}, 20, 10) |
0s |
passed |
| testRemoveNonUniqueMappings[3](GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S29M101S,20,2,20, chr1,137,+,130S64M,60,0,64], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S29M101S,20,2,20, chr1,137,+,130S64M,60,0,64], badMappings=[]}, 20, 10) |
0s |
passed |
| testRemoveNonUniqueMappings[4](GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S9M121S,40,0,9, chr1,137,+,130S64M,60,0,64], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr1,137,+,130S64M,60,0,64], badMappings=[chr2,1,-,64S9M121S,40,0,9]}, 20, 10) |
0.001s |
passed |
| testRemoveNonUniqueMappings[5](GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S10M120S,40,1,9, chr1,137,+,130S64M,60,0,64], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,1,+,100M94S,60,0,100, chr2,1,-,64S10M120S,40,1,9, chr1,137,+,130S64M,60,0,64], badMappings=[]}, 20, 10) |
0s |
passed |
| testRemoveNonUniqueMappings[6](GoodAndBadMappings{goodMappings=[chr1,10817090,+,854M1078S,60,3,843, chr8,6150682,-,1005S91M836S,0,3,76, chr11,48640941,+,906S55M971S,60,0,55, chr22,22585882,+,945S125M862S,20,0,125, chr1,10817996,+,1017S43M2I870M,60,2,895], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr1,10817090,+,854M1078S,60,3,843, chr22,22585882,+,945S125M862S,20,0,125, chr1,10817996,+,1017S43M2I870M,60,2,895], badMappings=[chr8,6150682,-,1005S91M836S,0,3,76, chr11,48640941,+,906S55M971S,60,0,55]}, 20, 40) |
0s |
passed |
| testSimpleChimeraWithStichableAlignmentsUnsortedInputs |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[0](chr8,38525855,-,525H36M7D70M,0,8,78, chr20,43927560,-,416H51M15D58M5I37M64H,60,20,94, false) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[1](chr20,43927560,-,416H51M15D58M5I37M64H,60,20,94, chr20,43927117,-,374M257S,60,3,359, false) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[2](chr20,43927479,-,342H74M7D69M146H,60,8,115, chr20,43927117,-,374M257S,60,3,359, false) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[3](chr1,1,+,100M50S,60,0,100, chr1,21,+,100S50M,60,0,50, false) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[4](chr1,1,+,100M50S,60,0,100, chr1,101,+,50S50M50S,60,0,50, false) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[5](chr1,1,+,100M50S,60,0,100, chr1,101,+,100S50M,60,0,50, true) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[6](chr20,43927560,-,416H51M15D58M5I37M64H,60,20,94, chr20,43927479,-,342H74M7D69M146H,60,8,115, true) |
0s |
passed |
| testSimpleChimeraWithStichableAlignments[7](chr1,1001001,+,100M1080S,60,0,100, chr1,1000001,-,80S1100M,60,0,1100, false) |
0s |
passed |
| testSortingAfterGapSplit[0](GoodAndBadMappings{goodMappings=[chr18,77371711,+,1447M50D184M980S,60,88,1375, chr18,77373176,+,1165H338M50I1058M,60,93,1115], badMappings=[]}, false, GoodAndBadMappings{goodMappings=[chr18,77371711,+,1447M1164S,60, chr18,77373176,+,1165H338M1108S,60, chr18,77373208,+,1447S184M980S,60, chr18,77373514,+,1165H388S1058M,60], badMappings=[]}) |
0.001s |
passed |
| testSplitGapsAndDropContainedAln[0](GoodAndBadMappings{goodMappings=[chr3,96003552,+,1137M58I16M438S,60,1079,58, chr3,96004627,+,1189H35M26I399M,60,392,204], badMappings=[]}, GoodAndBadMappings{goodMappings=[chr3,96003552,+,1137M512S,60, chr3,96004627,+,1189H35M26I399M,60,392,204], badMappings=[chr3,96004689,+,1195S16M438S,60]}) |
0s |
passed |
| testSplitGapsAndKeepChildrenTogether[0]((chr1,1000001,+,950M50S,60,0,950,chr1,1000101,+,100S300M200D600M,60,200,900), false, GoodAndBadMappings{goodMappings=[chr1,1000001,+,950M50S,60,0,950], badMappings=[chr1,1000101,+,100S300M600S,60, chr1,1000601,+,400S600M,60]}) |
0.001s |
passed |
| testSplitGapsAndKeepChildrenTogether[1]((chrUn_JTFH01000492v1_decoy,501,+,1097M6H,60,1,1092,chr17,26962248,-,121M1D142M1I165M62I130M482S,60,97,281), false, GoodAndBadMappings{goodMappings=[chrUn_JTFH01000492v1_decoy,501,+,1097M6H,60,1,1092], badMappings=[chr17,26962677,-,491S130M482S,60, chr17,26962248,-,121M1D142M1I165M674S,60]}) |
0s |
passed |
| testSplitGapsAndKeepChildrenTogether[2]((chr1,1000001,+,500M,60,0,500,chr1,1000101,+,100S300M200D600M,60,200,900), true, GoodAndBadMappings{goodMappings=[chr1,1000101,+,100S300M600S,60, chr1,1000601,+,400S600M,60], badMappings=[chr1,1000001,+,500M,60,0,500]}) |
0s |
passed |
| testSplitGapsAndKeepChildrenTogether[3]((chr1,1000001,+,500M,60,0,500,chr1,1000101,+,100S300M150I450M,60,150,750), true, GoodAndBadMappings{goodMappings=[chr1,1000101,+,100S300M600S,60, chr1,1000401,+,550S450M,60], badMappings=[chr1,1000001,+,500M,60,0,500]}) |
0s |
passed |