| Test |
Duration |
Result |
| testAssemblyBasedAnnotation[0]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@8a50c25e, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000060 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CTG_NAMES=simple_del_+, END=17000060, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-20, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.004s |
passed |
| testAssemblyBasedAnnotation[10]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@dca6f81f, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000078 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CTG_NAMES=simple_del_with_hom_+, END=17000078, HOMLEN=4, HOMSEQ=ATCG, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-38, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[11]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@a6c3b640, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000078 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CTG_NAMES=simple_del_with_hom_+, END=17000078, HOMLEN=4, HOMSEQ=ATCG, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-38, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[12]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@7302527f, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000050 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CONTRACTION=, CTG_NAMES=simple_del_dup_contraction_+, DUP_NUM=2,1, DUP_ORIENTATIONS=+, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000050, END=17000050, HOMLEN=10, HOMSEQ=CCCCCCCCCC, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-10, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[13]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@456cd9a0, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000050 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CONTRACTION=, CTG_NAMES=simple_del_dup_contraction_+, DUP_NUM=2,1, DUP_ORIENTATIONS=+, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000050, END=17000050, HOMLEN=10, HOMSEQ=CCCCCCCCCC, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-10, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[14]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@289b865, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=50, CTG_NAMES=simple_dup_exp_too_small_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000050, DUP_SEQ_CIGARS=10M,10M, END=17000040, EXPANSION=, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=50, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCC, SVLEN=10, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[15]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@d7eb7506, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=50, CTG_NAMES=simple_dup_exp_too_small_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000050, DUP_SEQ_CIGARS=10M,10M, END=17000040, EXPANSION=, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=50, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCC, SVLEN=10, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[16]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@7162db, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040 Q. of type=SYMBOLIC alleles=[G*, <DUP>] attr={ALIGN_LENGTHS=95, CTG_NAMES=simple_dup_exp_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000095, DUP_SEQ_CIGARS=55M,55M, END=17000040, EXPANSION=, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=95, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=55, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[17]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@d5d31f7c, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040 Q. of type=SYMBOLIC alleles=[G*, <DUP>] attr={ALIGN_LENGTHS=95, CTG_NAMES=simple_dup_exp_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:17000041-17000095, DUP_SEQ_CIGARS=55M,55M, END=17000040, EXPANSION=, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=95, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=55, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[18]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@7c756732, Broadcast(151), testSample, LINK, [[VC null @ 21:26849021 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={ALIGN_LENGTHS=1363, CTG_NAMES=simple_dup_exp_too_small_1_2_with_ins_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:26849022-26849037, DUP_SEQ_CIGARS=16M,16M, END=26849021, EXPANSION=, HQ_MAPPINGS=1, INSLEN=310, INSSEQ=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=1363, SEQ_ALT_HAPLOTYPE=CCGGGAAATGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCGGGAAATGCTTTTT, SVLEN=326, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[19]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@c3954635, Broadcast(151), testSample, LINK, [[VC null @ 21:26849021 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={ALIGN_LENGTHS=1363, CTG_NAMES=simple_dup_exp_too_small_1_2_with_ins_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:26849022-26849037, DUP_SEQ_CIGARS=16M,16M, END=26849021, EXPANSION=, HQ_MAPPINGS=1, INSLEN=310, INSSEQ=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=1363, SEQ_ALT_HAPLOTYPE=CCGGGAAATGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAGGCTCCGCCCCCTGGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCTCGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCGGGAAATGCTTTTT, SVLEN=326, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[1]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@59c413ff, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000060 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=40, CTG_NAMES=simple_del_+, END=17000060, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SVLEN=-20, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[20]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@e216be14, Broadcast(151), testSample, LINK, [[VC null @ 21:25297163 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=137, CTG_NAMES=simple_dup_exp_1_2_with_ins_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:25297164-25297252, DUP_SEQ_CIGARS=89M,89M, END=25297163, EXPANSION=, HQ_MAPPINGS=1, INSLEN=10, INSSEQ=CTCTCTCTCT, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=137, SEQ_ALT_HAPLOTYPE=AAAAGTAAATGTTATAAGAAATCTTAAGTATTATTTTCTTATGTTTCTAGCCTAATAAAGTGCTTTTATTAAAGCACTTTATTTAAAGGCTCTCTCTCTAAAAGTAAATGTTATAAGAAATCTTAAGTATTATTTTCTTATGTTTCTAGCCTAATAAAGTGCTTTTATTAAAGCACTTTATTTAAAGG, SVLEN=99, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[21]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@81b19995, Broadcast(151), testSample, LINK, [[VC null @ 21:25297163 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=137, CTG_NAMES=simple_dup_exp_1_2_with_ins_+, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=21:25297164-25297252, DUP_SEQ_CIGARS=89M,89M, END=25297163, EXPANSION=, HQ_MAPPINGS=1, INSLEN=10, INSSEQ=CTCTCTCTCT, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=137, SEQ_ALT_HAPLOTYPE=AAAAGTAAATGTTATAAGAAATCTTAAGTATTATTTTCTTATGTTTCTAGCCTAATAAAGTGCTTTTATTAAAGCACTTTATTTAAAGGCTCTCTCTCTAAAAGTAAATGTTATAAGAAATCTTAAGTATTATTTTCTTATGTTTCTAGCCTAATAAAGTGCTTTTATTAAAGCACTTTATTTAAAGG, SVLEN=99, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[22]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@3017d21e, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=127, CTG_NAMES=cpx_dup_exp_1_2_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312718, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312609, EXPANSION=, HOMLEN=13, HOMSEQ=GGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=127, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGAGGGCAGCTGTGGA, SVLEN=96, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[23]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@101ed17f, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=127, CTG_NAMES=cpx_dup_exp_1_2_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312718, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312609, EXPANSION=, HOMLEN=13, HOMSEQ=GGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=127, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGAGGGCAGCTGTGGA, SVLEN=96, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[24]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@62dfb23e, Broadcast(151), testSample, LINK, [[VC null @ 20:312609-312705 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=31, CONTRACTION=, CTG_NAMES=cpx_dup_contract_2_1_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312814, DUP_NUM=2,1, DUP_ORIENTATIONS=+, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312705, HOMLEN=109, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=31, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA, SVLEN=-96, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[25]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@266e499f, Broadcast(151), testSample, LINK, [[VC null @ 20:312609-312705 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=31, CONTRACTION=, CTG_NAMES=cpx_dup_contract_2_1_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312814, DUP_NUM=2,1, DUP_ORIENTATIONS=+, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312705, HOMLEN=109, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=31, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGCAGCTGTGGA, SVLEN=-96, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[26]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@c446f62a, Broadcast(151), testSample, LINK, [[VC null @ 20:312609-312705 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=31, CONTRACTION=, CTG_NAMES=cpx_dup_contract_3_2_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312897, DUP_NUM=3,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312705, HOMLEN=192, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=31, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA, SVLEN=-96, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[27]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@87d58d8b, Broadcast(151), testSample, LINK, [[VC null @ 20:312609-312705 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=31, CONTRACTION=, CTG_NAMES=cpx_dup_contract_3_2_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312897, DUP_NUM=3,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312705, HOMLEN=192, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=31, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGA, SVLEN=-96, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[28]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@a0dd02ae, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=127, CTG_NAMES=cpx_dup_exp_2_3_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312801, DUP_NUM=2,3, DUP_ORIENTATIONS=+++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312609, EXPANSION=, HOMLEN=96, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=127, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA, SVLEN=96, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[29]([DUP], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@80e4020f, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=127, CTG_NAMES=cpx_dup_exp_2_3_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312801, DUP_NUM=2,3, DUP_ORIENTATIONS=+++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312705, END=312609, EXPANSION=, HOMLEN=96, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=127, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCAGGAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGTCTCCACAGGAGGGCAAGGTGGACAATCTGTCCCATAGGAGGGGGATTCATGA, SVLEN=96, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[2]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@87bf6cc1, Broadcast(151), testSample, LINK, [[VC null @ 21:17000100 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_ins_+, END=17000100, HQ_MAPPINGS=1, INSLEN=50, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=100, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=50, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[30]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@9faf845f, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=73, CTG_NAMES=cpx_dup_exp_small_1_2_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312664, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312651, END=312609, EXPANSION=, HOMLEN=13, HOMSEQ=GGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=73, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGCAGCTGTGGA, SVLEN=42, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[31]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@7fb683c0, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=73, CTG_NAMES=cpx_dup_exp_small_1_2_pseudo_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312664, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312651, END=312609, EXPANSION=, HOMLEN=13, HOMSEQ=GGGCAGCTGTGGA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=73, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGCAGCTGTGGA, SVLEN=42, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[32]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@dfcb94c4, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=73, CTG_NAMES=cpx_dup_exp_too_small_2_3_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312693, DUP_NUM=2,3, DUP_ORIENTATIONS=+++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312651, END=312609, EXPANSION=, HOMLEN=42, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=73, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA, SVLEN=42, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[33]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@bfd29425, Broadcast(151), testSample, LINK, [[VC null @ 20:312609 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=73, CTG_NAMES=cpx_dup_exp_too_small_2_3_+, DUP_ANNOTATIONS_IMPRECISE=, DUP_IMPRECISE_AFFECTED_RANGE=20:312610-312693, DUP_NUM=2,3, DUP_ORIENTATIONS=+++, DUP_REPEAT_UNIT_REF_SPAN=20:312610-312651, END=312609, EXPANSION=, HOMLEN=42, HOMSEQ=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=73, SEQ_ALT_HAPLOTYPE=GGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAAGGGGAGCTGTGAAGAATGGAGCCAGTAATTAAATTCACTGAA, SVLEN=42, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[34]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@ab8ebf36, Broadcast(151), testSample, MATEID, [[VC null @ 21:17069296 Q. of type=SYMBOLIC alleles=[A*, AT]21:17069364]] attr={ALIGN_LENGTHS=50, CTG_NAMES=simple_inv_55_with_ins_+, HQ_MAPPINGS=1, INSLEN=1, INSSEQ=T, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_21_17069296_17069364_2, MAX_ALIGN_LENGTH=50, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 21:17069364 Q. of type=SYMBOLIC alleles=[G*, GA]21:17069296]] attr={ALIGN_LENGTHS=50, CTG_NAMES=simple_inv_55_with_ins_+, HQ_MAPPINGS=1, INSLEN=1, INSSEQ=T, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_21_17069296_17069364_1, MAX_ALIGN_LENGTH=50, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[35]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@1d396faf, Broadcast(151), testSample, MATEID, [[VC null @ 20:20248787 Q. of type=SYMBOLIC alleles=[C*, [20:20263493[C] attr={ALIGN_LENGTHS=1951, CTG_NAMES=simple_inv_33_with_hom_-, HOMLEN=654, HOMSEQ=GGAGGGAGGTGGGGGGGGTCAGCCCCCCGCCCAGCCAGCCGCCCCGTCCGGGAGGTGGGGGGTGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACCACCCCGTCTGGGAGGTGTACCCAACAGCTCATTGAGAACGGGCCATGATGACAATGGCAGTTTTGTGGAATAGAAACGGGGGAAAGGTGGGGAAAAGATTGAGAAATCGGATGGTTGCTGTGTCTGTGTAGAAAGAGGTAGACATGGGAGACTTCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATCCTGTTGACCTATGACCTTACCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCGGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTGTTGTCCTATGACCCTGCCAAATCCCCCTCTGCGAGAAACACCCAAGAATGATCAACTAAAAAAAAAAAAGAAAAAAGAAA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_20248787_20263493_2, MAX_ALIGN_LENGTH=1951, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 20:20263493 Q. of type=SYMBOLIC alleles=[G*, [20:20248787[G] attr={ALIGN_LENGTHS=1951, CTG_NAMES=simple_inv_33_with_hom_-, HOMLEN=654, HOMSEQ=GGAGGGAGGTGGGGGGGGTCAGCCCCCCGCCCAGCCAGCCGCCCCGTCCGGGAGGTGGGGGGTGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACCACCCCGTCTGGGAGGTGTACCCAACAGCTCATTGAGAACGGGCCATGATGACAATGGCAGTTTTGTGGAATAGAAACGGGGGAAAGGTGGGGAAAAGATTGAGAAATCGGATGGTTGCTGTGTCTGTGTAGAAAGAGGTAGACATGGGAGACTTCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATCCTGTTGACCTATGACCTTACCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCGGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTGTTGTCCTATGACCCTGCCAAATCCCCCTCTGCGAGAAACACCCAAGAATGATCAACTAAAAAAAAAAAAGAAAAAAGAAA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_20248787_20263493_1, MAX_ALIGN_LENGTH=1951, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[36]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@ab55aa1b, Broadcast(151), testSample, MATEID, [[VC null @ 20:200200 Q. of type=SYMBOLIC alleles=[C*, C]20:200605]] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_55_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_20_200200_200605_2, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 20:200605 Q. of type=SYMBOLIC alleles=[T*, T]20:200200]] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_55_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_20_200200_200605_1, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[37]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@9e81c0dc, Broadcast(151), testSample, MATEID, [[VC null @ 20:200200 Q. of type=SYMBOLIC alleles=[C*, C]20:200605]] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_55_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_20_200200_200605_2, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 20:200605 Q. of type=SYMBOLIC alleles=[T*, T]20:200200]] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_55_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV55=true, MAPPING_QUALITIES=60, MATEID=BND_INV55_20_200200_200605_1, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[38]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@8543f4fb, Broadcast(151), testSample, MATEID, [[VC null @ 20:200201 Q. of type=SYMBOLIC alleles=[A*, [20:200606[A] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_33_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_200201_200606_2, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 20:200606 Q. of type=SYMBOLIC alleles=[G*, [20:200201[G] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_33_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_200201_200606_1, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[39]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@78700bbc, Broadcast(151), testSample, MATEID, [[VC null @ 20:200201 Q. of type=SYMBOLIC alleles=[A*, [20:200606[A] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_33_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_200201_200606_2, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 20:200606 Q. of type=SYMBOLIC alleles=[G*, [20:200201[G] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_inv_33_with_hom_+, HOMLEN=5, HOMSEQ=ACACA, HQ_MAPPINGS=1, INV33=true, MAPPING_QUALITIES=60, MATEID=BND_INV33_20_200201_200606_1, MAX_ALIGN_LENGTH=100, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[3]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@4b55e862, Broadcast(151), testSample, LINK, [[VC null @ 21:17000100 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=100, CTG_NAMES=simple_ins_+, END=17000100, HQ_MAPPINGS=1, INSLEN=50, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=100, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=50, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[40]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@2aa88065, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28838813 Q. of type=SYMBOLIC alleles=[A*, ]chr20:29189401]A] attr={ALIGN_LENGTHS=119, CTG_NAMES=forIntraChromosomeRefOrderSwapWithHomology, HOMLEN=82, HOMSEQ=AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MATEID=BND_chr20_28838813_29189401_2, MAX_ALIGN_LENGTH=119, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr20:29189401 Q. of type=SYMBOLIC alleles=[G*, G[chr20:28838813[] attr={ALIGN_LENGTHS=119, CTG_NAMES=forIntraChromosomeRefOrderSwapWithHomology, HOMLEN=82, HOMSEQ=AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MATEID=BND_chr20_28838813_29189401_1, MAX_ALIGN_LENGTH=119, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[41]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@ad8a0018, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28838813 Q. of type=SYMBOLIC alleles=[A*, ]chr20:29189401]A] attr={ALIGN_LENGTHS=119, CTG_NAMES=forIntraChromosomeRefOrderSwapWithHomology, HOMLEN=82, HOMSEQ=AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MATEID=BND_chr20_28838813_29189401_2, MAX_ALIGN_LENGTH=119, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr20:29189401 Q. of type=SYMBOLIC alleles=[G*, G[chr20:28838813[] attr={ALIGN_LENGTHS=119, CTG_NAMES=forIntraChromosomeRefOrderSwapWithHomology, HOMLEN=82, HOMSEQ=AGTAGTTTCTCAGAATGCTTCTGCATAGTTTTTATGTGAAGATATTTCCTTCTACACTGTAGGCCTGAAAAGGCTCCAAATA, HQ_MAPPINGS=1, MAPPING_QUALITIES=60, MATEID=BND_chr20_28838813_29189401_1, MAX_ALIGN_LENGTH=119, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[42]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@36ca703b, Broadcast(152), testSample, MATEID, [[VC null @ chr20:44404789 Q. of type=SYMBOLIC alleles=[G*, ]chr20:44405064]TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGCG] attr={ALIGN_LENGTHS=62, CTG_NAMES=forIntraChromosomeRefOrderSwapWithInsertion, HQ_MAPPINGS=0, INSLEN=546, INSSEQ=TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC, MAPPING_QUALITIES=32, MATEID=BND_chr20_44404789_44405064_2, MAX_ALIGN_LENGTH=62, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr20:44405064 Q. of type=SYMBOLIC alleles=[G*, GTGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC[chr20:44404789[] attr={ALIGN_LENGTHS=62, CTG_NAMES=forIntraChromosomeRefOrderSwapWithInsertion, HQ_MAPPINGS=0, INSLEN=546, INSSEQ=TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC, MAPPING_QUALITIES=32, MATEID=BND_chr20_44404789_44405064_1, MAX_ALIGN_LENGTH=62, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[43]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@7119e0b8, Broadcast(152), testSample, MATEID, [[VC null @ chr20:44404789 Q. of type=SYMBOLIC alleles=[G*, ]chr20:44405064]TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGCG] attr={ALIGN_LENGTHS=62, CTG_NAMES=forIntraChromosomeRefOrderSwapWithInsertion, HQ_MAPPINGS=0, INSLEN=546, INSSEQ=TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC, MAPPING_QUALITIES=32, MATEID=BND_chr20_44404789_44405064_2, MAX_ALIGN_LENGTH=62, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr20:44405064 Q. of type=SYMBOLIC alleles=[G*, GTGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC[chr20:44404789[] attr={ALIGN_LENGTHS=62, CTG_NAMES=forIntraChromosomeRefOrderSwapWithInsertion, HQ_MAPPINGS=0, INSLEN=546, INSSEQ=TGGGTGTGTGCGTGTGTGTGTGACCGTGTGGAGTGTGTCTGTGTGCATGTGTGGGCTGTGTGGTGCGTGTGTGCTTATGTTTGGCGTGTGTGTGTGTGTGTGTGTGGACTGTGTGGTCTGTGTGTGTGTGCGTGTGTGTGGACTCTGTGGTGTGTGCATGTGTGCATGTATGTGCGTGTGTGTGACTGTGTGGTGTGTGTCTGTGTGCACGTGTGGGCTTATATTTGGTGTGTGTGCATGTGTGGACCGTGTGGTGTGTGTGTGTGCGTGTGTGGACTGTAGTGTGTGTGCACGTGTGTGTGTGCTTGTGTGTGGAGTGTGTGTGTGTGGACTGTAGTGTGTGTGCGTGACTGTGGTGTGTGTGCATGACTGTGTGGTGTGTGTGTGCATGTGTGTGGATTGTGTGGTGTGTGTGGACTGTGGGTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGTGTGTGTGCGTGTGTGGGGACTGTGTGGTGCGTGTGTGTGCTTGTGTGTGGACTGTGGATTGTGTGGTGTGTGTGTGCGCACGTGTGTGTGC, MAPPING_QUALITIES=32, MATEID=BND_chr20_44404789_44405064_1, MAX_ALIGN_LENGTH=62, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[44]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@e4da2bcd, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28766709 Q. of type=SYMBOLIC alleles=[C*, C[chr21:7969682[] attr={ALIGN_LENGTHS=166, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner, HOMLEN=156, HOMSEQ=TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG, HQ_MAPPINGS=0, MAPPING_QUALITIES=58, MATEID=BND_chr20_28766709_chr21_7969682_2, MAX_ALIGN_LENGTH=166, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:7969682 Q. of type=SYMBOLIC alleles=[T*, ]chr20:28766709]T] attr={ALIGN_LENGTHS=166, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner, HOMLEN=156, HOMSEQ=TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG, HQ_MAPPINGS=0, MAPPING_QUALITIES=58, MATEID=BND_chr20_28766709_chr21_7969682_1, MAX_ALIGN_LENGTH=166, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[45]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@35164005, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28766709 Q. of type=SYMBOLIC alleles=[C*, C[chr21:7969682[] attr={ALIGN_LENGTHS=237, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner, HOMLEN=156, HOMSEQ=TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG, HQ_MAPPINGS=0, MAPPING_QUALITIES=58, MATEID=BND_chr20_28766709_chr21_7969682_2, MAX_ALIGN_LENGTH=237, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:7969682 Q. of type=SYMBOLIC alleles=[T*, ]chr20:28766709]T] attr={ALIGN_LENGTHS=237, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner, HOMLEN=156, HOMSEQ=TTTGCAGATCCTACAAAATGACTGTTTCCAAACTGCTCAATCAAAACAAAGTTTCAACTCTGTCAGATGAATGCACACATCACAAAGAAATTTCTCAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCATAGGCCTCAAAG, HQ_MAPPINGS=0, MAPPING_QUALITIES=58, MATEID=BND_chr20_28766709_chr21_7969682_1, MAX_ALIGN_LENGTH=237, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[46]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@aaa38a2b, Broadcast(152), testSample, MATEID, [[VC null @ chr20:29286550 Q. of type=SYMBOLIC alleles=[T*, ]chr21:10806721]AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGTT] attr={ALIGN_LENGTHS=152, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner, HQ_MAPPINGS=0, INSLEN=40, INSSEQ=AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT, MAPPING_QUALITIES=22, MATEID=BND_chr20_29286550_chr21_10806721_2, MAX_ALIGN_LENGTH=152, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:10806721 Q. of type=SYMBOLIC alleles=[G*, GAGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT[chr20:29286550[] attr={ALIGN_LENGTHS=152, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner, HQ_MAPPINGS=0, INSLEN=40, INSSEQ=AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT, MAPPING_QUALITIES=22, MATEID=BND_chr20_29286550_chr21_10806721_1, MAX_ALIGN_LENGTH=152, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[47]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@9b252942, Broadcast(152), testSample, MATEID, [[VC null @ chr20:29286550 Q. of type=SYMBOLIC alleles=[T*, ]chr21:10806721]AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGTT] attr={ALIGN_LENGTHS=152, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner, HQ_MAPPINGS=0, INSLEN=40, INSSEQ=AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT, MAPPING_QUALITIES=22, MATEID=BND_chr20_29286550_chr21_10806721_2, MAX_ALIGN_LENGTH=152, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:10806721 Q. of type=SYMBOLIC alleles=[G*, GAGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT[chr20:29286550[] attr={ALIGN_LENGTHS=152, CTG_NAMES=forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner, HQ_MAPPINGS=0, INSLEN=40, INSSEQ=AGTCGAATTTCACACAGAATAATTTAGTTTCTCATAATGT, MAPPING_QUALITIES=22, MATEID=BND_chr20_29286550_chr21_10806721_1, MAX_ALIGN_LENGTH=152, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[48]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@f9f523c1, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28817977 Q. of type=SYMBOLIC alleles=[A*, AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA]chr21:10784829]] attr={ALIGN_LENGTHS=216, CTG_NAMES=forInterChromosomeStrandSwitch55, HQ_MAPPINGS=1, INSLEN=62, INSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA, MAPPING_QUALITIES=60, MATEID=BND_chr20_28817977_chr21_10784829_2, MAX_ALIGN_LENGTH=216, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:10784829 Q. of type=SYMBOLIC alleles=[T*, TTTTTTTTAATGTCTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT]chr20:28817977]] attr={ALIGN_LENGTHS=216, CTG_NAMES=forInterChromosomeStrandSwitch55, HQ_MAPPINGS=1, INSLEN=62, INSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA, MAPPING_QUALITIES=60, MATEID=BND_chr20_28817977_chr21_10784829_1, MAX_ALIGN_LENGTH=216, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[49]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@26d2dcfa, Broadcast(152), testSample, MATEID, [[VC null @ chr20:28817977 Q. of type=SYMBOLIC alleles=[A*, AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA]chr21:10784829]] attr={ALIGN_LENGTHS=216, CTG_NAMES=forInterChromosomeStrandSwitch55, HQ_MAPPINGS=1, INSLEN=62, INSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA, MAPPING_QUALITIES=60, MATEID=BND_chr20_28817977_chr21_10784829_2, MAX_ALIGN_LENGTH=216, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:10784829 Q. of type=SYMBOLIC alleles=[T*, TTTTTTTTAATGTCTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT]chr20:28817977]] attr={ALIGN_LENGTHS=216, CTG_NAMES=forInterChromosomeStrandSwitch55, HQ_MAPPINGS=1, INSLEN=62, INSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAGACATTAAAAAAA, MAPPING_QUALITIES=60, MATEID=BND_chr20_28817977_chr21_10784829_1, MAX_ALIGN_LENGTH=216, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[4]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@e5f7cd7a, Broadcast(151), testSample, LINK, [[VC null @ 21:17000070-17000130 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_fudged_del_+, END=17000130, HQ_MAPPINGS=1, INSLEN=10, INSSEQ=CCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SEQ_ALT_HAPLOTYPE=CCCCCCCCCC, SVLEN=-60, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[50]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@b283a3b0, Broadcast(152), testSample, MATEID, [[VC null @ chr20:29204769 Q. of type=SYMBOLIC alleles=[A*, [chr21:7229448[A] attr={ALIGN_LENGTHS=260, CTG_NAMES=forInterChromosomeStrandSwitch33, HOMLEN=155, HOMSEQ=ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC, HQ_MAPPINGS=0, MAPPING_QUALITIES=25, MATEID=BND_chr20_29204769_chr21_7229448_2, MAX_ALIGN_LENGTH=260, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:7229448 Q. of type=SYMBOLIC alleles=[A*, [chr20:29204769[A] attr={ALIGN_LENGTHS=260, CTG_NAMES=forInterChromosomeStrandSwitch33, HOMLEN=155, HOMSEQ=ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC, HQ_MAPPINGS=0, MAPPING_QUALITIES=25, MATEID=BND_chr20_29204769_chr21_7229448_1, MAX_ALIGN_LENGTH=260, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[51]([BND, BND], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@f4a6075f, Broadcast(152), testSample, MATEID, [[VC null @ chr20:29204769 Q. of type=SYMBOLIC alleles=[A*, [chr21:7229448[A] attr={ALIGN_LENGTHS=260, CTG_NAMES=forInterChromosomeStrandSwitch33, HOMLEN=155, HOMSEQ=ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC, HQ_MAPPINGS=0, MAPPING_QUALITIES=25, MATEID=BND_chr20_29204769_chr21_7229448_2, MAX_ALIGN_LENGTH=260, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr21:7229448 Q. of type=SYMBOLIC alleles=[A*, [chr20:29204769[A] attr={ALIGN_LENGTHS=260, CTG_NAMES=forInterChromosomeStrandSwitch33, HOMLEN=155, HOMSEQ=ATTTCATTGAACAGATTGGAAACACTCTTTCTGTAGAATCTGCAATGGACATTTTTCGCACTTTGAGGCCTATGGTGGAAAAGGAAATATCTTCACATAAAAACTAGACCAAAGCATTCTGACAAACTTCTTTGTGATGTGTGCATTCATCTCAC, HQ_MAPPINGS=0, MAPPING_QUALITIES=25, MATEID=BND_chr20_29204769_chr21_7229448_1, MAX_ALIGN_LENGTH=260, SVTYPE=BND, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[5]([DEL], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@a0a8a89b, Broadcast(151), testSample, LINK, [[VC null @ 21:17000070-17000130 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_fudged_del_+, END=17000130, HQ_MAPPINGS=1, INSLEN=10, INSSEQ=CCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SEQ_ALT_HAPLOTYPE=CCCCCCCCCC, SVLEN=-60, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[6]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@f279465f, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000060 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=40, CTG_NAMES=rpl_fat_ins_+, END=17000060, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=60, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[7]([INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@c1ec9800, Broadcast(151), testSample, LINK, [[VC null @ 21:17000040-17000060 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={ALIGN_LENGTHS=40, CTG_NAMES=rpl_fat_ins_+, END=17000060, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=40, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=60, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testAssemblyBasedAnnotation[8]([DEL, INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@aa515b59, Broadcast(151), testSample, LINK, [[VC null @ 21:17000070-17000130 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_linked_del_ins_+, END=17000130, HQ_MAPPINGS=1, LINK=INS_21_17000070_17000070, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SVLEN=-60, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 21:17000070 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_linked_del_ins_+, END=17000070, HQ_MAPPINGS=1, INSLEN=55, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, LINK=DEL_21_17000070_17000130, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=55, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testAssemblyBasedAnnotation[9]([DEL, INS], org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence@6502367a, Broadcast(151), testSample, LINK, [[VC null @ 21:17000070-17000130 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_linked_del_ins_+, END=17000130, HQ_MAPPINGS=1, LINK=INS_21_17000070_17000070, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SVLEN=-60, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ 21:17000070 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=70, CTG_NAMES=rpl_linked_del_ins_+, END=17000070, HQ_MAPPINGS=1, INSLEN=55, INSSEQ=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, LINK=DEL_21_17000070_17000130, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=70, SEQ_ALT_HAPLOTYPE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC, SVLEN=55, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testMiscCases |
0.011s |
passed |
| testProcessEvidenceTargetLinks[0]([EvidenceTargetLink{source=StrandedInterval{interval=0[190:210], strand=true}, target=StrandedInterval{interval=0[310:320], strand=false}, splitReads=5, readPairs=7}], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, SVTYPE=DEL} GT=[] filters=], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, READ_PAIR_SUPPORT=7, SPLIT_READ_SUPPORT=5, SVTYPE=DEL} GT=[] filters=]) |
0.282s |
passed |
| testProcessEvidenceTargetLinks[1]([EvidenceTargetLink{source=StrandedInterval{interval=0[190:210], strand=true}, target=StrandedInterval{interval=0[310:320], strand=true}, splitReads=5, readPairs=7}], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, SVTYPE=DEL} GT=[] filters=], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, SVTYPE=DEL} GT=[] filters=]) |
0.001s |
passed |
| testProcessEvidenceTargetLinks[2]([EvidenceTargetLink{source=StrandedInterval{interval=0[190:210], strand=true}, target=StrandedInterval{interval=0[310:320], strand=false}, splitReads=3, readPairs=4}, EvidenceTargetLink{source=StrandedInterval{interval=0[192:215], strand=true}, target=StrandedInterval{interval=0[299:303], strand=false}, splitReads=2, readPairs=3}], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, SVTYPE=DEL} GT=[] filters=], [[VC null @ 20:200-300 Q. of type=SYMBOLIC alleles=[N*, <DEL>] attr={END=300, READ_PAIR_SUPPORT=7, SPLIT_READ_SUPPORT=5, SVTYPE=DEL} GT=[] filters=]) |
0.001s |
passed |
| testProduceCIInterval[0](200, 1[190:225], -10,25, null) |
0s |
passed |
| testProduceCIInterval[1](200, 1[200:225], 0,25, null) |
0s |
passed |
| testProduceCIInterval[2](200, 1[201:225], null, java.lang.IllegalStateException: Interval must contain point) |
0s |
passed |