| Test |
Duration |
Result |
| testBreakpointComplicationsAndLocationAndAltSeqInference[0](SimpleChimera{sourceContigName='simple_del_+', regionWithLowerCoordOnContig=21,17000001,+,40M40S,60,0,100, regionWithHigherCoordOnContig=21,17000061,+,40S40M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@bef3ffc, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000060-17000060 NO_SWITCH homology: inserted sequence: ) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[10](SimpleChimera{sourceContigName='simple_del_with_hom_+', regionWithLowerCoordOnContig=21,17000001,+,44M40S,60,0,100, regionWithHigherCoordOnContig=21,17000079,+,40S44M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@b28fd1, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000078-17000078 NO_SWITCH homology: ATCG inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[11](SimpleChimera{sourceContigName='simple_del_with_hom_-', regionWithLowerCoordOnContig=21,17000079,-,40S44M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,44M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4f123e4e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000078-17000078 NO_SWITCH homology: ATCG inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[12](SimpleChimera{sourceContigName='simple_del_dup_contraction_+', regionWithLowerCoordOnContig=21,17000001,+,50M40S,60,0,100, regionWithHigherCoordOnContig=21,17000051,+,40S50M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@886adc3, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000050-17000050 NO_SWITCH homology: CCCCCCCCCC inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000050 ref repeat num: 2 ctg repeat num: 1 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+] precise cigarStringsForDupSeqOnCtg: ) |
0.004s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[13](SimpleChimera{sourceContigName='simple_del_dup_contraction_-', regionWithLowerCoordOnContig=21,17000051,-,40S50M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,50M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7f941f5a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000050-17000050 NO_SWITCH homology: CCCCCCCCCC inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000050 ref repeat num: 2 ctg repeat num: 1 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+] precise cigarStringsForDupSeqOnCtg: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[14](SimpleChimera{sourceContigName='simple_dup_exp_too_small_+', regionWithLowerCoordOnContig=21,17000001,+,50M50S,60,0,100, regionWithHigherCoordOnContig=21,17000041,+,50S50M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@237c65fc, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000040-17000040 NO_SWITCH homology: inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000050 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [10M, 10M]) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[15](SimpleChimera{sourceContigName='simple_dup_exp_too_small_-', regionWithLowerCoordOnContig=21,17000041,-,50S50M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,50M50S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@24c39ce3, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000040-17000040 NO_SWITCH homology: inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000050 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [10M, 10M]) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[16](SimpleChimera{sourceContigName='simple_dup_exp_+', regionWithLowerCoordOnContig=21,17000001,+,95M95S,60,0,100, regionWithHigherCoordOnContig=21,17000041,+,95S95M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@22ad2191, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000040-17000040 NO_SWITCH homology: inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000095 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [55M, 55M]) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[17](SimpleChimera{sourceContigName='simple_dup_exp_-', regionWithLowerCoordOnContig=21,17000041,-,95S95M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,95M95S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@726ad245, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000040-17000040 NO_SWITCH homology: inserted sequence: tandem duplication repeat unit ref span: 21:17000041-17000095 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [55M, 55M]) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[18](SimpleChimera{sourceContigName='simple_dup_exp_too_small_1_2_with_ins_+', regionWithLowerCoordOnContig=21,26847644,+,1394M1675S,60,1,1389, regionWithHigherCoordOnContig=21,26849022,+,1704H657M2I706M,60,2,1345, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@728594e9, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:26849021-26849021 21:26849021-26849021 NO_SWITCH homology: inserted sequence: TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC tandem duplication repeat unit ref span: 21:26849022-26849037 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [16M, 16M]) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[19](SimpleChimera{sourceContigName='simple_dup_exp_too_small_1_2_with_ins_-', regionWithLowerCoordOnContig=21,26849022,-,1704H657M3I706M,60,3,1344, regionWithHigherCoordOnContig=21,26847644,-,1394M1676S,60,1,1384, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@191dd84a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:26849021-26849021 21:26849021-26849021 NO_SWITCH homology: inserted sequence: TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC tandem duplication repeat unit ref span: 21:26849022-26849037 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [16M, 16M]) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[1](SimpleChimera{sourceContigName='simple_del_-', regionWithLowerCoordOnContig=21,17000061,-,40S40M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,40M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@79bd2d87, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000060-17000060 NO_SWITCH homology: inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[20](SimpleChimera{sourceContigName='simple_dup_exp_1_2_with_ins_+', regionWithLowerCoordOnContig=21,25297101,+,152M147S,60,0,100, regionWithHigherCoordOnContig=21,25297164,+,162S137M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@b4e52a4, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:25297163-25297163 21:25297163-25297163 NO_SWITCH homology: inserted sequence: CTCTCTCTCT tandem duplication repeat unit ref span: 21:25297164-25297252 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [89M, 89M]) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[21](SimpleChimera{sourceContigName='simple_dup_exp_1_2_with_ins_-', regionWithLowerCoordOnContig=21,25297164,-,162S137M,60,0,100, regionWithHigherCoordOnContig=21,25297101,-,152M147S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7ba87d24, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:25297163-25297163 21:25297163-25297163 NO_SWITCH homology: inserted sequence: CTCTCTCTCT tandem duplication repeat unit ref span: 21:25297164-25297252 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] precise cigarStringsForDupSeqOnCtg: [89M, 89M]) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[22](SimpleChimera{sourceContigName='cpx_dup_exp_1_2_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,140M135S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,127S148M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@6461e6ba, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] imprecise:) |
0.007s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[23](SimpleChimera{sourceContigName='cpx_dup_exp_1_2_pseudo_-', regionWithLowerCoordOnContig=20,312610,-,127S148M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,140M135S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@54dfde5b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] imprecise:) |
0.004s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[24](SimpleChimera{sourceContigName='cpx_dup_contract_2_1_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,140M39S,60,0,100, regionWithHigherCoordOnContig=20,312706,+,31S148M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@131d4b13, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312705-312705 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 2 ctg repeat num: 1 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+] imprecise:) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[25](SimpleChimera{sourceContigName='cpx_dup_contract_2_1_pseudo_-', regionWithLowerCoordOnContig=20,312706,-,31S148M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,140M39S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@48e8de7b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312705-312705 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 2 ctg repeat num: 1 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+] imprecise:) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[26](SimpleChimera{sourceContigName='cpx_dup_contract_3_2_+', regionWithLowerCoordOnContig=20,312579,+,223M39S,60,0,100, regionWithHigherCoordOnContig=20,312706,+,31S231M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4a572677, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312705-312705 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 3 ctg repeat num: 2 dupSeqStrandOnRef: [+, +, +] dupSeqStrandOnCtg: [+, +] imprecise:) |
0.003s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[27](SimpleChimera{sourceContigName='cpx_dup_contract_3_2_-', regionWithLowerCoordOnContig=20,312706,-,31S231M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,223M39S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@26f9165b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312705-312705 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 3 ctg repeat num: 2 dupSeqStrandOnRef: [+, +, +] dupSeqStrandOnCtg: [+, +] imprecise:) |
0.003s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[28](SimpleChimera{sourceContigName='cpx_dup_exp_2_3_+', regionWithLowerCoordOnContig=20,312579,+,223M135S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,127S231M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@1764625a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 2 ctg repeat num: 3 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+, +, +] imprecise:) |
0.003s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[29](SimpleChimera{sourceContigName='cpx_dup_exp_2_3_-', regionWithLowerCoordOnContig=20,312610,-,127S231M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,223M135S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@3f832bd, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312705 ref repeat num: 2 ctg repeat num: 3 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+, +, +] imprecise:) |
0.002s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[2](SimpleChimera{sourceContigName='simple_ins_+', regionWithLowerCoordOnContig=21,17000001,+,100M100S,60,0,100, regionWithHigherCoordOnContig=21,17000101,+,100S100M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@5c273b3e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000100-17000100 21:17000100-17000100 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[30](SimpleChimera{sourceContigName='cpx_dup_exp_small_1_2_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,86M81S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,73S94M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@6cf87ba6, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312651 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] imprecise:) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[31](SimpleChimera{sourceContigName='cpx_dup_exp_small_1_2_pseudo_-', regionWithLowerCoordOnContig=20,312610,-,73S94M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,86M81S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@2c5281b1, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGCAGCTGTGGA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312651 ref repeat num: 1 ctg repeat num: 2 dupSeqStrandOnRef: [+] dupSeqStrandOnCtg: [+, +] imprecise:) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[32](SimpleChimera{sourceContigName='cpx_dup_exp_too_small_2_3_+', regionWithLowerCoordOnContig=20,312579,+,115M81S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,73S123M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@3e4c4911, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312651 ref repeat num: 2 ctg repeat num: 3 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+, +, +] imprecise:) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[33](SimpleChimera{sourceContigName='cpx_dup_exp_too_small_2_3_-', regionWithLowerCoordOnContig=20,312610,-,73S123M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,115M81S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7d7d6131, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:312609-312609 20:312609-312609 NO_SWITCH homology: GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA inserted sequence: tandem duplication repeat unit ref span: 20:312610-312651 ref repeat num: 2 ctg repeat num: 3 dupSeqStrandOnRef: [+, +] dupSeqStrandOnCtg: [+, +, +] imprecise:) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[34](SimpleChimera{sourceContigName='simple_inv_55_with_ins_+', regionWithLowerCoordOnContig=21,17069151,+,146M51S,60,0,100, regionWithHigherCoordOnContig=21,17069315,-,50M147S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@33df44cd, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17069296-17069296 21:17069364-17069364 FORWARD_TO_REVERSE homology: inserted sequence: T) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[35](SimpleChimera{sourceContigName='simple_inv_33_with_hom_-', regionWithLowerCoordOnContig=20,20262839,-,3603H24M1I611M1I1970M,60,8,2561, regionWithHigherCoordOnContig=20,20248787,+,1953S10M3I9M1I246M2D1572M1I798M5D730M1I347M4I535M,60,41,4068, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7a48e086, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:20248787-20248787 20:20263493-20263493 REVERSE_TO_FORWARD homology: GGAGGGAGGTGGGGGGGGTCAGCCCCCCGCCCAGCCAGCCGCCCCGTCCGGGAGGTGGGGGGTGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACCACCCCGTCTGGGAGGTGTACCCAACAGCTCATTGAGAACGGGCCATGATGACAATGGCAGTTTTGTGGAATAGAAACGGGGGAAAGGTGGGGAAAAGATTGAGAAATCGGATGGTTGCTGTGTCTGTGTAGAAAGAGGTAGACATGGGAGACTTCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATCCTGTTGACCTATGACCTTACCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCGGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTGTTGTCCTATGACCCTGCCAAATCCCCCTCTGCGAGAAACACCCAAGAATGATCAACTAAAAAAAAAAAAGAAAAAAGAAA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[36](SimpleChimera{sourceContigName='simple_inv_55_with_hom_+', regionWithLowerCoordOnContig=20,200101,+,105M100S,60,0,100, regionWithHigherCoordOnContig=20,200501,-,105M100S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@507a3fee, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:200200-200200 20:200605-200605 FORWARD_TO_REVERSE homology: ACACA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[37](SimpleChimera{sourceContigName='simple_inv_55_with_hom_-', regionWithLowerCoordOnContig=20,200501,+,105M100S,60,0,100, regionWithHigherCoordOnContig=20,200101,-,105M100S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@61a01e85, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:200200-200200 20:200605-200605 FORWARD_TO_REVERSE homology: ACACA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[38](SimpleChimera{sourceContigName='simple_inv_33_with_hom_+', regionWithLowerCoordOnContig=20,200201,-,100S105M,60,0,100, regionWithHigherCoordOnContig=20,200601,+,100S105M,60,0,100, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@637f8b01, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:200201-200201 20:200606-200606 REVERSE_TO_FORWARD homology: ACACA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[39](SimpleChimera{sourceContigName='simple_inv_33_with_hom_-', regionWithLowerCoordOnContig=20,200601,-,100S105M,60,0,100, regionWithHigherCoordOnContig=20,200201,+,100S105M,60,0,100, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@e30d60, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 20:200201-200201 20:200606-200606 REVERSE_TO_FORWARD homology: ACACA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[3](SimpleChimera{sourceContigName='simple_ins_-', regionWithLowerCoordOnContig=21,17000101,-,100S100M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,100M100S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7038781f, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000100-17000100 21:17000100-17000100 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[40](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithHomology', regionWithLowerCoordOnContig=chr20,29189283,+,201M637S,60,5,180, regionWithHigherCoordOnContig=chr20,28838813,+,119H719M,60,25,594, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@48cec56d, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28838813-28838813 chr20:29189401-29189401 NO_SWITCH homology: AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[41](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithHomology', regionWithLowerCoordOnContig=chr20,28838813,-,119S719M,60,25,594, regionWithHigherCoordOnContig=chr20,29189283,-,201M637H,60,5,180, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@303bcad6, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28838813-28838813 chr20:29189401-29189401 NO_SWITCH homology: AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[42](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithInsertion', regionWithLowerCoordOnContig=chr20,44405003,+,9H62M696H,32,3,47, regionWithHigherCoordOnContig=chr20,44404789,+,617S66M2I82M,60,4,45, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4ed03796, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:44404789-44404789 chr20:44405064-44405064 NO_SWITCH homology: inserted sequence: TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[43](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithInsertion', regionWithLowerCoordOnContig=chr20,44404789,-,617S66M2I82M,60,4,45, regionWithHigherCoordOnContig=chr20,44405003,-,9H62M696H,32,3,47, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@28be98fc, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:44404789-44404789 chr20:44405064-44405064 NO_SWITCH homology: inserted sequence: TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[44](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner', regionWithLowerCoordOnContig=chr20,28766544,+,322M332H,58,9,277, regionWithHigherCoordOnContig=chr21,7969682,+,166S211M1I276M,58,33,310, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@653408dc, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28766709-28766709 chr21:7969682-7969682 NO_SWITCH homology: TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[45](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner', regionWithLowerCoordOnContig=chr21,7969682,-,525H211M1I182M,58,23,266, regionWithHigherCoordOnContig=chr20,28766185,-,681M238S,58,7,646, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@685e8e30, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28766709-28766709 chr21:7969682-7969682 NO_SWITCH homology: TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG inserted sequence: ) |
0.001s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[46](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner', regionWithLowerCoordOnContig=chr21,10806570,+,152M908H,22,14,82, regionWithHigherCoordOnContig=chr20,29286550,+,192S604M1I263M,60,33,690, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@311eb977, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:29286550-29286550 chr21:10806721-10806721 NO_SWITCH homology: inserted sequence: AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[47](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner', regionWithLowerCoordOnContig=chr20,29286550,-,263M1I604M192S,60,33,690, regionWithHigherCoordOnContig=chr21,10806570,-,908H152M,22,14,82, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@56290dd0, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:29286550-29286550 chr21:10806721-10806721 NO_SWITCH homology: inserted sequence: AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[48](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch55', regionWithLowerCoordOnContig=chr21,10784600,+,230M279S,60,12,170, regionWithHigherCoordOnContig=chr20,28817762,-,123M1I93M292H,60,11,149, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7bfc43a8, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28817977-28817977 chr21:10784829-10784829 FORWARD_TO_REVERSE homology: inserted sequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[49](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch55', regionWithLowerCoordOnContig=chr20,28817762,+,123M1I93M292H,60,11,149, regionWithHigherCoordOnContig=chr21,10784600,-,230M279S,60,12,170, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@58100e7d, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:28817977-28817977 chr21:10784829-10784829 FORWARD_TO_REVERSE homology: inserted sequence: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[4](SimpleChimera{sourceContigName='rpl_fudged_del_+', regionWithLowerCoordOnContig=21,17000001,+,70M80S,60,0,70, regionWithHigherCoordOnContig=21,17000131,+,80S70M,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@13869c39, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000070-17000070 21:17000130-17000130 NO_SWITCH homology: inserted sequence: CCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[50](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch33', regionWithLowerCoordOnContig=chr20,29204769,-,260S530M,58,2,520, regionWithHigherCoordOnContig=chr21,7229293,+,375H110M1D44M1I260M,25,57,105, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@2ad4ade7, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:29204769-29204769 chr21:7229448-7229448 REVERSE_TO_FORWARD homology: ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[51](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch33', regionWithLowerCoordOnContig=chr21,7229293,-,375H110M1D44M1I260M,25,57,105, regionWithHigherCoordOnContig=chr20,29204769,+,260S530M,58,2,520, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@79c7d95a, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), chr20:29204769-29204769 chr21:7229448-7229448 REVERSE_TO_FORWARD homology: ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC inserted sequence: ) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[5](SimpleChimera{sourceContigName='rpl_fudged_del_-', regionWithLowerCoordOnContig=21,17000131,-,80S70M,60,0,70, regionWithHigherCoordOnContig=21,17000001,-,70M80S,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@d9d2c3e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000070-17000070 21:17000130-17000130 NO_SWITCH homology: inserted sequence: CCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[6](SimpleChimera{sourceContigName='rpl_fat_ins_+', regionWithLowerCoordOnContig=21,17000001,+,40M100S,60,0,60, regionWithHigherCoordOnContig=21,17000061,+,100S40M,60,0,60, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@31e376e4, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000060-17000060 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[7](SimpleChimera{sourceContigName='rpl_fat_ins_-', regionWithLowerCoordOnContig=21,17000061,-,100S40M,60,0,60, regionWithHigherCoordOnContig=21,17000001,-,40M100S,60,0,60, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@593a017e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000040-17000040 21:17000060-17000060 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[8](SimpleChimera{sourceContigName='rpl_linked_del_ins_+', regionWithLowerCoordOnContig=21,17000001,+,70M125S,60,0,70, regionWithHigherCoordOnContig=21,17000131,+,125S70M,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7fd1342c, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000070-17000070 21:17000130-17000130 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0s |
passed |
| testBreakpointComplicationsAndLocationAndAltSeqInference[9](SimpleChimera{sourceContigName='rpl_linked_del_ins_-', regionWithLowerCoordOnContig=21,17000131,-,125S70M,60,0,70, regionWithHigherCoordOnContig=21,17000001,-,70M125S,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@5a5684ea, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), 21:17000070-17000070 21:17000130-17000130 NO_SWITCH homology: inserted sequence: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC) |
0s |
passed |
| testExtractCigarAndAltSeqForSimpleTandup_complicated |
0s |
passed |
| testGetInferenceClass[0](SimpleChimera{sourceContigName='simple_del_+', regionWithLowerCoordOnContig=21,17000001,+,40M40S,60,0,100, regionWithHigherCoordOnContig=21,17000061,+,40S40M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@bef3ffc, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[10](SimpleChimera{sourceContigName='simple_del_with_hom_+', regionWithLowerCoordOnContig=21,17000001,+,44M40S,60,0,100, regionWithHigherCoordOnContig=21,17000079,+,40S44M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@b28fd1, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[11](SimpleChimera{sourceContigName='simple_del_with_hom_-', regionWithLowerCoordOnContig=21,17000079,-,40S44M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,44M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4f123e4e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[12](SimpleChimera{sourceContigName='simple_del_dup_contraction_+', regionWithLowerCoordOnContig=21,17000001,+,50M40S,60,0,100, regionWithHigherCoordOnContig=21,17000051,+,40S50M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@886adc3, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[13](SimpleChimera{sourceContigName='simple_del_dup_contraction_-', regionWithLowerCoordOnContig=21,17000051,-,40S50M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,50M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7f941f5a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[14](SimpleChimera{sourceContigName='simple_dup_exp_too_small_+', regionWithLowerCoordOnContig=21,17000001,+,50M50S,60,0,100, regionWithHigherCoordOnContig=21,17000041,+,50S50M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@237c65fc, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[15](SimpleChimera{sourceContigName='simple_dup_exp_too_small_-', regionWithLowerCoordOnContig=21,17000041,-,50S50M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,50M50S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@24c39ce3, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[16](SimpleChimera{sourceContigName='simple_dup_exp_+', regionWithLowerCoordOnContig=21,17000001,+,95M95S,60,0,100, regionWithHigherCoordOnContig=21,17000041,+,95S95M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@22ad2191, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[17](SimpleChimera{sourceContigName='simple_dup_exp_-', regionWithLowerCoordOnContig=21,17000041,-,95S95M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,95M95S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@726ad245, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[18](SimpleChimera{sourceContigName='simple_dup_exp_too_small_1_2_with_ins_+', regionWithLowerCoordOnContig=21,26847644,+,1394M1675S,60,1,1389, regionWithHigherCoordOnContig=21,26849022,+,1704H657M2I706M,60,2,1345, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@728594e9, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[19](SimpleChimera{sourceContigName='simple_dup_exp_too_small_1_2_with_ins_-', regionWithLowerCoordOnContig=21,26849022,-,1704H657M3I706M,60,3,1344, regionWithHigherCoordOnContig=21,26847644,-,1394M1676S,60,1,1384, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@191dd84a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[1](SimpleChimera{sourceContigName='simple_del_-', regionWithLowerCoordOnContig=21,17000061,-,40S40M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,40M40S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@79bd2d87, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[20](SimpleChimera{sourceContigName='simple_dup_exp_1_2_with_ins_+', regionWithLowerCoordOnContig=21,25297101,+,152M147S,60,0,100, regionWithHigherCoordOnContig=21,25297164,+,162S137M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@b4e52a4, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[21](SimpleChimera{sourceContigName='simple_dup_exp_1_2_with_ins_-', regionWithLowerCoordOnContig=21,25297164,-,162S137M,60,0,100, regionWithHigherCoordOnContig=21,25297101,-,152M147S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7ba87d24, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithPreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[22](SimpleChimera{sourceContigName='cpx_dup_exp_1_2_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,140M135S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,127S148M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@6461e6ba, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[23](SimpleChimera{sourceContigName='cpx_dup_exp_1_2_pseudo_-', regionWithLowerCoordOnContig=20,312610,-,127S148M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,140M135S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@54dfde5b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[24](SimpleChimera{sourceContigName='cpx_dup_contract_2_1_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,140M39S,60,0,100, regionWithHigherCoordOnContig=20,312706,+,31S148M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@131d4b13, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[25](SimpleChimera{sourceContigName='cpx_dup_contract_2_1_pseudo_-', regionWithLowerCoordOnContig=20,312706,-,31S148M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,140M39S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@48e8de7b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[26](SimpleChimera{sourceContigName='cpx_dup_contract_3_2_+', regionWithLowerCoordOnContig=20,312579,+,223M39S,60,0,100, regionWithHigherCoordOnContig=20,312706,+,31S231M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4a572677, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[27](SimpleChimera{sourceContigName='cpx_dup_contract_3_2_-', regionWithLowerCoordOnContig=20,312706,-,31S231M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,223M39S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@26f9165b, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[28](SimpleChimera{sourceContigName='cpx_dup_exp_2_3_+', regionWithLowerCoordOnContig=20,312579,+,223M135S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,127S231M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@1764625a, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[29](SimpleChimera{sourceContigName='cpx_dup_exp_2_3_-', regionWithLowerCoordOnContig=20,312610,-,127S231M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,223M135S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@3f832bd, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[2](SimpleChimera{sourceContigName='simple_ins_+', regionWithLowerCoordOnContig=21,17000001,+,100M100S,60,0,100, regionWithHigherCoordOnContig=21,17000101,+,100S100M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@5c273b3e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[30](SimpleChimera{sourceContigName='cpx_dup_exp_small_1_2_pseudo_+', regionWithLowerCoordOnContig=20,312579,+,86M81S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,73S94M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@6cf87ba6, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[31](SimpleChimera{sourceContigName='cpx_dup_exp_small_1_2_pseudo_-', regionWithLowerCoordOnContig=20,312610,-,73S94M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,86M81S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@2c5281b1, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[32](SimpleChimera{sourceContigName='cpx_dup_exp_too_small_2_3_+', regionWithLowerCoordOnContig=20,312579,+,115M81S,60,0,100, regionWithHigherCoordOnContig=20,312610,+,73S123M,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@3e4c4911, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[33](SimpleChimera{sourceContigName='cpx_dup_exp_too_small_2_3_-', regionWithLowerCoordOnContig=20,312610,-,73S123M,60,0,100, regionWithHigherCoordOnContig=20,312579,-,115M81S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7d7d6131, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SmallDuplicationWithImpreciseDupRangeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[34](SimpleChimera{sourceContigName='simple_inv_55_with_ins_+', regionWithLowerCoordOnContig=21,17069151,+,146M51S,60,0,100, regionWithHigherCoordOnContig=21,17069315,-,50M147S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@33df44cd, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0s |
passed |
| testGetInferenceClass[35](SimpleChimera{sourceContigName='simple_inv_33_with_hom_-', regionWithLowerCoordOnContig=20,20262839,-,3603H24M1I611M1I1970M,60,8,2561, regionWithHigherCoordOnContig=20,20248787,+,1953S10M3I9M1I246M2D1572M1I798M5D730M1I347M4I535M,60,41,4068, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7a48e086, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0s |
passed |
| testGetInferenceClass[36](SimpleChimera{sourceContigName='simple_inv_55_with_hom_+', regionWithLowerCoordOnContig=20,200101,+,105M100S,60,0,100, regionWithHigherCoordOnContig=20,200501,-,105M100S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@507a3fee, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0.001s |
passed |
| testGetInferenceClass[37](SimpleChimera{sourceContigName='simple_inv_55_with_hom_-', regionWithLowerCoordOnContig=20,200501,+,105M100S,60,0,100, regionWithHigherCoordOnContig=20,200101,-,105M100S,60,0,100, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@61a01e85, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0s |
passed |
| testGetInferenceClass[38](SimpleChimera{sourceContigName='simple_inv_33_with_hom_+', regionWithLowerCoordOnContig=20,200201,-,100S105M,60,0,100, regionWithHigherCoordOnContig=20,200601,+,100S105M,60,0,100, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@637f8b01, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0s |
passed |
| testGetInferenceClass[39](SimpleChimera{sourceContigName='simple_inv_33_with_hom_-', regionWithLowerCoordOnContig=20,200601,-,100S105M,60,0,100, regionWithHigherCoordOnContig=20,200201,+,100S105M,60,0,100, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@e30d60, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrStrandSwitchBreakpointInference) |
0s |
passed |
| testGetInferenceClass[3](SimpleChimera{sourceContigName='simple_ins_-', regionWithLowerCoordOnContig=21,17000101,-,100S100M,60,0,100, regionWithHigherCoordOnContig=21,17000001,-,100M100S,60,0,100, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7038781f, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[40](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithHomology', regionWithLowerCoordOnContig=chr20,29189283,+,201M637S,60,5,180, regionWithHigherCoordOnContig=chr20,28838813,+,119H719M,60,25,594, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@48cec56d, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrRefOrderSwapBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[41](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithHomology', regionWithLowerCoordOnContig=chr20,28838813,-,119S719M,60,25,594, regionWithHigherCoordOnContig=chr20,29189283,-,201M637H,60,5,180, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@303bcad6, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrRefOrderSwapBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[42](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithInsertion', regionWithLowerCoordOnContig=chr20,44405003,+,9H62M696H,32,3,47, regionWithHigherCoordOnContig=chr20,44404789,+,617S66M2I82M,60,4,45, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@4ed03796, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrRefOrderSwapBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[43](SimpleChimera{sourceContigName='forIntraChromosomeRefOrderSwapWithInsertion', regionWithLowerCoordOnContig=chr20,44404789,-,617S66M2I82M,60,4,45, regionWithHigherCoordOnContig=chr20,44405003,-,9H62M696H,32,3,47, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@28be98fc, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$IntraChrRefOrderSwapBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[44](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner', regionWithLowerCoordOnContig=chr20,28766544,+,322M332H,58,9,277, regionWithHigherCoordOnContig=chr21,7969682,+,166S211M1I276M,58,33,310, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@653408dc, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[45](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner', regionWithLowerCoordOnContig=chr21,7969682,-,525H211M1I182M,58,23,266, regionWithHigherCoordOnContig=chr20,28766185,-,681M238S,58,7,646, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@685e8e30, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[46](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner', regionWithLowerCoordOnContig=chr21,10806570,+,152M908H,22,14,82, regionWithHigherCoordOnContig=chr20,29286550,+,192S604M1I263M,60,33,690, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@311eb977, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[47](SimpleChimera{sourceContigName='forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner', regionWithLowerCoordOnContig=chr20,29286550,-,263M1I604M192S,60,33,690, regionWithHigherCoordOnContig=chr21,10806570,-,908H152M,22,14,82, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@56290dd0, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[48](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch55', regionWithLowerCoordOnContig=chr21,10784600,+,230M279S,60,12,170, regionWithHigherCoordOnContig=chr20,28817762,-,123M1I93M292H,60,11,149, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7bfc43a8, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[49](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch55', regionWithLowerCoordOnContig=chr20,28817762,+,123M1I93M292H,60,11,149, regionWithHigherCoordOnContig=chr21,10784600,-,230M279S,60,12,170, strandSwitch=FORWARD_TO_REVERSE, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@58100e7d, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[4](SimpleChimera{sourceContigName='rpl_fudged_del_+', regionWithLowerCoordOnContig=21,17000001,+,70M80S,60,0,70, regionWithHigherCoordOnContig=21,17000131,+,80S70M,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@13869c39, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[50](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch33', regionWithLowerCoordOnContig=chr20,29204769,-,260S530M,58,2,520, regionWithHigherCoordOnContig=chr21,7229293,+,375H110M1D44M1I260M,25,57,105, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@2ad4ade7, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[51](SimpleChimera{sourceContigName='forInterChromosomeStrandSwitch33', regionWithLowerCoordOnContig=chr21,7229293,-,375H110M1D44M1I260M,25,57,105, regionWithHigherCoordOnContig=chr20,29204769,+,260S530M,58,2,520, strandSwitch=REVERSE_TO_FORWARD, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@79c7d95a, SAMSequenceDictionary:( sequences:13 length:112493195 md5:43393ce9ee3231cb0e7af55511326dac), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$InterChromosomeBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[5](SimpleChimera{sourceContigName='rpl_fudged_del_-', regionWithLowerCoordOnContig=21,17000131,-,80S70M,60,0,70, regionWithHigherCoordOnContig=21,17000001,-,70M80S,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@d9d2c3e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[6](SimpleChimera{sourceContigName='rpl_fat_ins_+', regionWithLowerCoordOnContig=21,17000001,+,40M100S,60,0,60, regionWithHigherCoordOnContig=21,17000061,+,100S40M,60,0,60, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@31e376e4, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[7](SimpleChimera{sourceContigName='rpl_fat_ins_-', regionWithLowerCoordOnContig=21,17000061,-,100S40M,60,0,60, regionWithHigherCoordOnContig=21,17000001,-,40M100S,60,0,60, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@593a017e, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0.001s |
passed |
| testGetInferenceClass[8](SimpleChimera{sourceContigName='rpl_linked_del_ins_+', regionWithLowerCoordOnContig=21,17000001,+,70M125S,60,0,70, regionWithHigherCoordOnContig=21,17000131,+,125S70M,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=true, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@7fd1342c, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testGetInferenceClass[9](SimpleChimera{sourceContigName='rpl_linked_del_ins_-', regionWithLowerCoordOnContig=21,17000131,-,125S70M,60,0,70, regionWithHigherCoordOnContig=21,17000001,-,70M125S,60,0,70, strandSwitch=NO_SWITCH, isForwardStrandRepresentation=false, insertionMappings=[], goodNonCanonicalMappingSATag='NONE'}, [B@5a5684ea, SAMSequenceDictionary:( sequences:2 length:111155415 md5:6105eaf82ce1eebc05f2d1d4f54c059c), class org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference$SimpleInsertionDeletionBreakpointsInference) |
0s |
passed |
| testValidateInferredLocations[0](chr20:10000-10000, chr20:9999-9999, SAMSequenceDictionary:( sequences:3366 length:3217346917 md5:5de1aef8e9e3be34ae7696779a4791c7)) |
0.003s |
passed |
| testValidateInferredLocations[1](chr20:64444168-64444168, chr20:64444168-64444168, SAMSequenceDictionary:( sequences:3366 length:3217346917 md5:5de1aef8e9e3be34ae7696779a4791c7)) |
0.002s |
passed |
| testValidateInferredLocations[2](chr20:10000-10000, chr21:46709984-46709984, SAMSequenceDictionary:( sequences:3366 length:3217346917 md5:5de1aef8e9e3be34ae7696779a4791c7)) |
0.002s |
passed |