| Test |
Duration |
Result |
| testDeletionConsistencyCheck[0]([VC null @ chr6:857169-857562 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={END=857562, SVLEN=-393, SVTYPE=DEL} GT=[] filters=, [], false) |
0s |
passed |
| testDeletionConsistencyCheck[1]([VC null @ chr6:857169-857562 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={END=857562, SVLEN=-393, SVTYPE=DEL} GT=[] filters=, [chr6:857170-857564, chr6:857767-857852], true) |
0s |
passed |
| testDeletionConsistencyCheck[2]([VC null @ chr6:857169-857562 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={END=857562, SVLEN=-393, SVTYPE=DEL} GT=[] filters=, [chr6:857767-857852], false) |
0s |
passed |
| testGetInsFromOneEnd[0](true, 4, chr1:100-100, A*, [30, 40, 50, 10], [1, 2, 3, 4, 1, 2, 3, 4], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=131, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[10](false, 2, chr1:100-100, A*, [20], [1, -chrX:10001-10009, 1], true, null) |
0s |
passed |
| testGetInsFromOneEnd[1](false, 7, chr1:100-100, A*, [30, 40, 50, 10], [1, 2, 3, 4, 1, 2, 3, 4], true, null) |
0s |
passed |
| testGetInsFromOneEnd[2](true, 2, chr1:100-100, A*, [30, 40, 50, 10], [UINS-50, -chrX:10001-10009, 1, 2, 3, 3, 1, 4], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=60, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[3](false, 5, chr1:100-100, A*, [30, 40, 50, 10], [1, 2, 3, 3, 1, 4, UINS-49], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=50, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[4](false, 5, chr1:100-100, A*, [30, 40, 50, 10], [1, 2, 3, 3, 1, 4, UINS-49], false, null) |
0s |
passed |
| testGetInsFromOneEnd[5](true, 1, chr1:100-100, A*, [20], [UINS-100, 1], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=101, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[6](false, 0, chr1:100-100, A*, [20], [1, UINS-100], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=101, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[7](true, 2, chr1:100-100, A*, [20], [1, -chrX:10001-10039, 1], true, [VC null @ chr1:100 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=100, SVLEN=60, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testGetInsFromOneEnd[8](true, 2, chr1:100-100, A*, [20], [1, -chrX:10001-10009, 1], true, null) |
0s |
passed |
| testGetInsFromOneEnd[9](false, 2, chr1:100-100, A*, [20], [1, -chrX:10001-10039, 1], true, null) |
0s |
passed |
| testGetInsLen[0](UINS-12, [], 12) |
0s |
passed |
| testGetInsLen[1](UINS-12, [89], 12) |
0s |
passed |
| testGetInsLen[2](3, [30, 40, 50, 10], 50) |
0s |
passed |
| testGetInsLen[3](-4, [30, 40, 50, 10], 10) |
0s |
passed |
| testGetInsLen[4](chr1:1000-1000, [30, 40, 50, 10], 1) |
0s |
passed |
| testGetInsLen[5](chr1:1000-1001, [30, 40, 50, 10], 2) |
0s |
passed |
| testGetInsLen[6](-chr1:1001-1050, [30, 40, 50, 10], 50) |
0s |
passed |
| testGetMissingAndPresentAndInvertedSegments[0]([chr1:1001-1100], [-1], ([],[],[1])) |
0.001s |
passed |
| testGetMissingAndPresentAndInvertedSegments[1]([chr1:1001-1100, chr1:1100-1200, chr1:1200-1300, chr1:1300-1400], [1, 3, 4], ([chr1:1100-1200],[1, 3, 4],[])) |
0s |
passed |
| testGetMissingAndPresentAndInvertedSegments[2]([chr1:1001-1100, chr1:1100-1200, chr1:1200-1300, chr1:1300-1400], [1, 4, 2, 3], ([],[1, 2, 3, 4],[])) |
0s |
passed |
| testGetMissingAndPresentAndInvertedSegments[3]([chr1:1001-1100, chr1:1100-1200, chr1:1200-1300, chr1:1300-1400], [-4, 1, 3, 2], ([],[1, 2, 3],[4])) |
0s |
passed |
| testGetMissingAndPresentAndInvertedSegments[4]([chr1:1001-1100, chr1:1100-1200, chr1:1200-1300, chr1:1300-1400], [1, 3, 4, -1], ([chr1:1100-1200],[1, 3, 4],[1])) |
0.001s |
passed |
| testIsConsistentWithCPX[0]([VC null @ chr1:4939534-4939614 Q. of type=SYMBOLIC alleles=[A*, <INV>] attr={END=4939614, SVLEN=0, SVTYPE=INV} GT=[] filters=, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$RelevantAttributes@2235ab04, false) |
0s |
passed |
| testIsConsistentWithCPX[1]([VC null @ chr1:4939507 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=4939507, SVLEN=59, SVTYPE=INS} GT=[] filters=, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$RelevantAttributes@2235ab04, true) |
0s |
passed |
| testIsConsistentWithCPX[2]([VC null @ chr1:4939535-4939614 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={END=4939614, SVLEN=-79, SVTYPE=DEL} GT=[] filters=, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$RelevantAttributes@2235ab04, false) |
0s |
passed |
| testIsConsistentWithCPX[3]([VC null @ chr6:857169-857562 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={END=857562, SVLEN=-393, SVTYPE=DEL} GT=[] filters=, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$RelevantAttributes@2a178b15, true) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorCompactifyMissingSegments[0]([chr1:10012-10020, chr1:10000-10010], [chr1:10000-10010, chr1:10012-10020]) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorCompactifyMissingSegments[1]([chr1:10011-10020, chr1:10000-10010], [chr1:10000-10020]) |
0.001s |
passed |
| testMultiSegmentsCpxVariantExtractorCompactifyMissingSegments[2]([chr1:10010-10020, chr1:10000-10010], [chr1:10000-10020]) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorFindAllSegments[0]([UINS-58, 1, 2, 2], 2, 1) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorFindAllSegments[1]([UINS-58, 1, 2, 2], 3, -1) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorFindAllSegments[2]([UINS-58, 1, 2, 3, 1, chrX:10000-10200, 1, 3, 3, UINS-15], 3, 1) |
0s |
passed |
| testMultiSegmentsCpxVariantExtractorFindAllSegments[3]([UINS-58, 1, 2, 3, 1, chrX:10000-10200, 1, 2, 3, UINS-15], 3, 6) |
0s |
passed |
| testPostProcessConvertReplacementToFatInsOrInsAndDel[0]([VC null @ chr9:108455205-108455252 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={END=108455252, INSLEN=7, INSSEQ=ATCTTAT, SVLEN=-47, SVTYPE=DEL} GT=[] filters=, []) |
0.001s |
passed |
| testPostProcessConvertReplacementToFatInsOrInsAndDel[1]([VC null @ chr21:23428920-23428967 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={ALIGN_LENGTHS=56,56, CPX_EVENT=CPX_chr21:23428920-23429023, CTG_NAMES=asm029052:tig00000,asm029052:tig00001, END=23428967, HQ_MAPPINGS=2, INSLEN=85, INSSEQ=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA, INSSEQ_MAP=1330_1385_chr21:23428968-23429023_+_1329H56M1200H_49_4_36_O,1330_1385_chr21:23428968-23429023_+_1329H56M1200H_49_4_36_O, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=56, SEQ_ALT_HAPLOTYPE=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA, SVLEN=-47, SVTYPE=DEL, TOTAL_MAPPINGS=2} GT=[] filters=, [[VC null @ chr21:23428920-23428967 Q. of type=SYMBOLIC alleles=[TTTATATAAATATATATAAATATATAATATATAATAATATAATATAAT*, <INS>] attr={ALIGN_LENGTHS=56,56, CPX_EVENT=CPX_chr21:23428920-23429023, CTG_NAMES=asm029052:tig00000,asm029052:tig00001, END=23428967, HQ_MAPPINGS=2, INSLEN=85, INSSEQ=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=56, SEQ_ALT_HAPLOTYPE=ATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATA, SVLEN=85, SVTYPE=INS, TOTAL_MAPPINGS=2} GT=[] filters=]) |
0.001s |
passed |
| testPostProcessConvertReplacementToFatInsOrInsAndDel[2]([VC null @ chr20:63093346-63094245 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=942, CPX_EVENT=CPX_chr20:63092255-63094246, CTG_NAMES=asm028762:tig00002, END=63094245, HQ_MAPPINGS=1, INSLEN=1, INSSEQ=T, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=942, SEQ_ALT_HAPLOTYPE=T, SVLEN=-899, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=, [[VC null @ chr20:63093346-63094245 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={ALIGN_LENGTHS=942, CPX_EVENT=CPX_chr20:63092255-63094246, CTG_NAMES=asm028762:tig00002, END=63094245, HQ_MAPPINGS=1, INSLEN=1, INSSEQ=T, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=942, SEQ_ALT_HAPLOTYPE=T, SVLEN=-899, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.001s |
passed |
| testPostProcessConvertReplacementToFatInsOrInsAndDel[3]([VC null @ chr20:440444-440697 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={ALIGN_LENGTHS=170, CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=440697, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=TTCATACACACACAGATACACACCCGCGCACACACAGATGCACACACACACCCGTACACT, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=170, SEQ_ALT_HAPLOTYPE=TTCATACACACACAGATACACACCCGCGCACACACAGATGCACACACACACCCGTACACT, SVLEN=-253, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=, [[VC null @ chr20:440444 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={ALIGN_LENGTHS=170, CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=440444, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=TTCATACACACACAGATACACACCCGCGCACACACAGATGCACACACACACCCGTACACT, LINK=DEL_chr20_440444_440697_CPX_DERIVED, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=170, SEQ_ALT_HAPLOTYPE=TTCATACACACACAGATACACACCCGCGCACACACAGATGCACACACACACCCGTACACT, SVLEN=60, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr20:440444-440697 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={ALIGN_LENGTHS=170, CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=440697, HQ_MAPPINGS=1, LINK=INS_chr20_440444_440444_CPX_DERIVED, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=170, SVLEN=-253, SVTYPE=DEL, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0s |
passed |
| testPostProcessConvertShortDupToIns[0]([VC null @ chr1:10000-10100 Q. of type=SYMBOLIC alleles=[A*, <INV>] attr={END=10100, SVLEN=0, SVTYPE=INV} GT=[] filters=, [VC null @ chr1:10000-10100 Q. of type=SYMBOLIC alleles=[A*, <INV>] attr={END=10100, SVLEN=0, SVTYPE=INV} GT=[] filters=) |
0s |
passed |
| testPostProcessConvertShortDupToIns[1]([VC null @ chr1:10001-10100 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={END=10100, SVLEN=-99, SVTYPE=DEL} GT=[] filters=, [VC null @ chr1:10001-10100 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={END=10100, SVLEN=-99, SVTYPE=DEL} GT=[] filters=) |
0s |
passed |
| testPostProcessConvertShortDupToIns[2]([VC null @ chr1:11111 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=11111, SVLEN=100, SVTYPE=INS} GT=[] filters=, [VC null @ chr1:11111 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={END=11111, SVLEN=100, SVTYPE=INS} GT=[] filters=) |
0s |
passed |
| testPostProcessConvertShortDupToIns[3]([VC null @ chr2:241987322 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=1125, CPX_EVENT=CPX_chr2:241987323-241987529, CTG_NAMES=asm004634:tig00000, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=chr2:241987323-241987529, DUP_SEQ_CIGARS=207M,207M, END=241987322, EXPANSION=, HQ_MAPPINGS=1, INSLEN=196, INSSEQ=AGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGCTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCAGTGTACTCGGAGATCTAGTCGATGGC, INSSEQ_MAP=1102_1242_chr2:241987361-241987501_-_1101H141M1284H_60_8_101_O,1176_1373_chr2:241987323-241987520_-_1175H198M1153H_60_12_138_O, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=1125, SEQ_ALT_HAPLOTYPE=GTTGGGTGTACTCGGAGATCCGGTCGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGCTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCAGTGTACTCGGAGATCTAGTCGATGGCGTTGGGTGTACTCGGAGATCCAGTTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGTGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCATTGTACTCGGAGATCCAGTCGATGGCGTTGGGTGTACTTGGAGATCCAGTCGGTGGCGTTGGGTGTACTTGGAGATCC, SVLEN=403, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr2:241987322 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=1125, CPX_EVENT=CPX_chr2:241987323-241987529, CTG_NAMES=asm004634:tig00000, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=chr2:241987323-241987529, DUP_SEQ_CIGARS=207M,207M, END=241987322, EXPANSION=, HQ_MAPPINGS=1, INSLEN=196, INSSEQ=AGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGCTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCAGTGTACTCGGAGATCTAGTCGATGGC, INSSEQ_MAP=1102_1242_chr2:241987361-241987501_-_1101H141M1284H_60_8_101_O,1176_1373_chr2:241987323-241987520_-_1175H198M1153H_60_12_138_O, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=1125, SEQ_ALT_HAPLOTYPE=GTTGGGTGTACTCGGAGATCCGGTCGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCGGAGATCCAGTGGATGGCGTTGGGTGTACTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGCTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGCGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCAGTGTACTCGGAGATCTAGTCGATGGCGTTGGGTGTACTCGGAGATCCAGTTGATGGCATTCAGCGTACTCGGAGATCCAGTTGATGGTGTTGGGTGTTCTCGGAGATCCAGTCGGTGGTGTTGGGTGTACTCAGAGATCCAGTTGATGGCATTCATTGTACTCGGAGATCCAGTCGATGGCGTTGGGTGTACTTGGAGATCCAGTCGGTGGCGTTGGGTGTACTTGGAGATCC, SVLEN=403, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=) |
0.001s |
passed |
| testPostProcessConvertShortDupToIns[4]([VC null @ chr2:83340906 Q. of type=SYMBOLIC alleles=[T*, <DUP>] attr={ALIGN_LENGTHS=58, CPX_EVENT=CPX_chr2:83340902-83340950, CTG_NAMES=asm003204:tig00000, DUP_NUM=1,2, DUP_ORIENTATIONS=+-, DUP_REPEAT_UNIT_REF_SPAN=chr2:83340907-83340950, DUP_SEQ_CIGARS=44M,44M, END=83340906, EXPANSION=, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=TTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAA, INSSEQ_MAP=1280_1328_chr2:83340902-83340950_+_1279H49M62H_60_0_49_O, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=58, SEQ_ALT_HAPLOTYPE=TATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATATTATAATATATTTTAATATTATATTATATTATAATATATT, SVLEN=104, SVTYPE=DUP, TOTAL_MAPPINGS=1} GT=[] filters=, [VC null @ chr2:83340906 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={ALIGN_LENGTHS=58, CPX_EVENT=CPX_chr2:83340902-83340950, CTG_NAMES=asm003204:tig00000, DUP_NUM=1,2, DUP_ORIENTATIONS=+-, DUP_REPEAT_UNIT_REF_SPAN=chr2:83340907-83340950, DUP_SEQ_CIGARS=44M,44M, END=83340906, EXPANSION=, HQ_MAPPINGS=1, INSLEN=60, INSSEQ=TTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAA, INSSEQ_MAP=1280_1328_chr2:83340902-83340950_+_1279H49M62H_60_0_49_O, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=58, SEQ_ALT_HAPLOTYPE=TATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATTATATTATATTATAATATATTTTAATATATTATAATATATTTTAATATTATATTATATTATAATATATT, SVLEN=104, SVTYPE=INS, TOTAL_MAPPINGS=1} GT=[] filters=) |
0s |
passed |
| testRemoveDuplicates[0]([[VC null @ chr21:46069065 Q. of type=SYMBOLIC alleles=[C*, <INS>] attr={CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069065, SVLEN=60, SVTYPE=INS} GT=[] filters=, [VC null @ chr21:46069156-46069208 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069208, SVLEN=-52, SVTYPE=DEL} GT=[] filters=, [VC null @ chr20:439692 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=439692, SVLEN=130, SVTYPE=INS} GT=[] filters=, [VC null @ chr20:439692-440161 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=440161, SVLEN=-469, SVTYPE=DEL} GT=[] filters=, [VC null @ chr21:187497345-187497595 Q. of type=SYMBOLIC alleles=[A*, <INV>] attr={CPX_EVENT=CPX_chr1:187495696-187497598, CTG_NAMES=asm001762:tig00000,asm001762:tig00001,asm001763:tig00000, END=187497595, SVLEN=0, SVTYPE=INV} GT=[] filters=], [[VC null @ chr21:46069065 Q. of type=SYMBOLIC alleles=[C*, <INS>] attr={ALIGN_LENGTHS=91,91, CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069065, HQ_MAPPINGS=2, INSLEN=60, INSSEQ=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=91, SEQ_ALT_HAPLOTYPE=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT, SVLEN=60, SVTYPE=INS, TOTAL_MAPPINGS=2} GT=[] filters=, [VC null @ chr21:46069156-46069208 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={ALIGN_LENGTHS=91,91, CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069208, HQ_MAPPINGS=2, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=91, SVLEN=-52, SVTYPE=DEL, TOTAL_MAPPINGS=2} GT=[] filters=, [VC null @ chr20:56839685 Q. of type=SYMBOLIC alleles=[A*, <DUP>] attr={ALIGN_LENGTHS=770, CPX_EVENT=CPX_chrY:56838784-56839794, CTG_NAMES=asm031346:tig00004, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=chrY:56839686-56839794, DUP_SEQ_CIGARS=109M,109M, END=56839685, EXPANSION=, HQ_MAPPINGS=1, INSLEN=95, INSSEQ=CTGTTGACTAGTCTTTGCCTACAGAGGGCGTTGTGACATATCTCTGCACTGATCTCTCAGGTGAGGTAACTTCTCTAGTCTCTGCCTACAGAGGG, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=770, SEQ_ALT_HAPLOTYPE=CATTGTGACTTATCTCTGCACTGATCACCCAGGTGATGTAACTCTTGTCTAGGCTCTGGCCACAGGGACATAGTGACATATATCTGCACTGATCACACAGGTAATGTAACTGTTGACTAGTCTTTGCCTACAGAGGGCGTTGTGACATATCTCTGCACTGATCTCTCAGGTGAGGTAACTTCTCTAGTCTCTGCCTACAGAGGGCATTGTGACATCACTCTGCAATGATCACCCAGGTGATGTAACTCTTGTCTAGGCTCTGCCTACATGGACATTGTGACATGTCTCTGCACTGATCACCCAGGTGATGTAA, TOTAL_MAPPINGS=1} GT=[] filters=], [[VC null @ chr21:46069065 Q. of type=SYMBOLIC alleles=[C*, <INS>] attr={ALIGN_LENGTHS=91,91, CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069065, HQ_MAPPINGS=2, INSLEN=60, INSSEQ=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=91, SEQ_ALT_HAPLOTYPE=CTAGGTGTGTGCATGTGTGCACACGTGTGTGCATGTGTGTGCATGTGTGCACACGTGTGT, SVLEN=60, SVTYPE=INS, TOTAL_MAPPINGS=2} GT=[] filters=, [VC null @ chr21:46069156-46069208 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={ALIGN_LENGTHS=91,91, CPX_EVENT=CPX_chr21:46069065-46069209, CTG_NAMES=asm029362:tig00001,asm029362:tig00002, END=46069208, HQ_MAPPINGS=2, MAPPING_QUALITIES=60,60, MAX_ALIGN_LENGTH=91, SVLEN=-52, SVTYPE=DEL, TOTAL_MAPPINGS=2} GT=[] filters=, [VC null @ chr20:439692 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=439692, SVLEN=130, SVTYPE=INS} GT=[] filters=, [VC null @ chr20:439692-440161 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={CPX_EVENT=CPX_chrX:439692-440698, CTG_NAMES=asm030101:tig00001, END=440161, SVLEN=-469, SVTYPE=DEL} GT=[] filters=, [VC null @ chr21:187497345-187497595 Q. of type=SYMBOLIC alleles=[A*, <INV>] attr={CPX_EVENT=CPX_chr1:187495696-187497598, CTG_NAMES=asm001762:tig00000,asm001762:tig00001,asm001763:tig00000, END=187497595, SVLEN=0, SVTYPE=INV} GT=[] filters=, [VC null @ chr20:56839685 Q. of type=SYMBOLIC alleles=[A*, <DUP>] attr={ALIGN_LENGTHS=770, CPX_EVENT=CPX_chrY:56838784-56839794, CTG_NAMES=asm031346:tig00004, DUP_NUM=1,2, DUP_ORIENTATIONS=++, DUP_REPEAT_UNIT_REF_SPAN=chrY:56839686-56839794, DUP_SEQ_CIGARS=109M,109M, END=56839685, EXPANSION=, HQ_MAPPINGS=1, INSLEN=95, INSSEQ=CTGTTGACTAGTCTTTGCCTACAGAGGGCGTTGTGACATATCTCTGCACTGATCTCTCAGGTGAGGTAACTTCTCTAGTCTCTGCCTACAGAGGG, MAPPING_QUALITIES=60, MAX_ALIGN_LENGTH=770, SEQ_ALT_HAPLOTYPE=CATTGTGACTTATCTCTGCACTGATCACCCAGGTGATGTAACTCTTGTCTAGGCTCTGGCCACAGGGACATAGTGACATATATCTGCACTGATCACACAGGTAATGTAACTGTTGACTAGTCTTTGCCTACAGAGGGCGTTGTGACATATCTCTGCACTGATCTCTCAGGTGAGGTAACTTCTCTAGTCTCTGCCTACAGAGGGCATTGTGACATCACTCTGCAATGATCACCCAGGTGATGTAACTCTTGTCTAGGCTCTGCCTACATGGACATTGTGACATGTCTCTGCACTGATCACCCAGGTGATGTAA, TOTAL_MAPPINGS=1} GT=[] filters=]) |
0.003s |
passed |
| testSegmentedCpxVariantExtractor[0]([VC null @ chr20:51740560-51740561 Q. of type=SYMBOLIC alleles=[AT*, <CPX>] attr={ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496, CTG_NAMES=asm028558:tig00002,asm028558:tig00003, END=51740561, MAPPING_QUALITIES=16,51,8, MAX_ALIGN_LENGTH=435, SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGT, SVLEN=549, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:51740560 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr20:51740560-51740561, CTG_NAMES=asm028558:tig00002,asm028558:tig00003, END=51740560, MAPPING_QUALITIES=16,51,8, MAX_ALIGN_LENGTH=435, SVLEN=549, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[10]([VC null @ chr20:61919906-61920109 Q. of type=SYMBOLIC alleles=[T*, <CPX>] attr={ALT_ARRANGEMENT=1,2,3,UINS-177,1,2,2,3, CTG_NAMES=asm028707:tig00000, END=61920109, MAPPING_QUALITIES=15,19, MAX_ALIGN_LENGTH=2835, SEGMENTS=chr20:61919906-61919908,chr20:61919908-61920054,chr20:61920054-61920109, SEQ_ALT_HAPLOTYPE=TCGTGATTATGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGCGGTGATTGCATGGAAGTGTGGTGTCACAGTGATTGCGTGGAAGCGTGTCGTGATTGTGTGGAAGCATGGTATCGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTGTGATTGTGTGGAAGCATGGTATCGTGATTGTGGAAGCGTGGTATCGCGGCGATTGTGTGGAAGCGTGGTGTCGCAGTGATTGCGTGGAAGCATGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGTGTGGAAGCATGGTGTCGTGATTGTGTGGAAGCATGTCGTGATTGTGTGGAAGTGTGATGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATTGGAAGTGTGGTGTCACGCTGATTGCATGGAAGTGTGTTGTGATTGTGTGGAAGCGTGATATCGCAGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGTGTGGAAGCGTGGTGTCACGGTGATTGCGTGGAAGCGTGTTGTGATTGTGTGGAAGCGTGGTATCGTGATCGGAAGCGTGGTGTTGCGGTGATTGCATGGAAGCATGTTGTGATTGTGTGGAAGCATGGTATCGTGATTGTCTGGAAGCATGGTGTCATGGTGATTGGAAGTGTGTCGTGATTG, SVLEN=541, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:61920109 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={CPX_EVENT=CPX_chr20:61919906-61920109, CTG_NAMES=[asm028707:tig00000], END=61920109, MAPPING_QUALITIES=15,19, MAX_ALIGN_LENGTH=2835, SVLEN=531, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[11]([VC null @ chr20:38653054-38653283 Q. of type=SYMBOLIC alleles=[T*, <CPX>] attr={ALT_ARRANGEMENT=1,2,3,4,3,1,2,3,4,5,2,3,4,5, CTG_NAMES=asm028418:tig00000, END=38653283, MAPPING_QUALITIES=46,28, MAX_ALIGN_LENGTH=1478, SEGMENTS=chr20:38653054-38653113,chr20:38653113-38653145,chr20:38653145-38653179,chr20:38653179-38653273,chr20:38653273-38653283, SEQ_ALT_HAPLOTYPE=TGGTGGTGGTGGTGATGGAAATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGATGGTGGTGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGGTGATAATGATGGTAGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGGTGATGGAAATGATGATGATGTTAATTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGGTGGTGTTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGGTGATGGTGATGATGATTATGATGGTGGTGGTGGTGGTGGTGGTGCTGGTGATAGTGGTGGTGGTGGTGCTGGTGATGATAATGGTGGTGGTGGTGATGATGGTGATGATGATTATGATGGTGGTGTTGGTGGTGCTGGTGATGATAATCATGCTGGTGGTGGTGGCGTTGATGATGGTGACAGTAGTGGTGATGATGGTGGTGGTGGTGATGGAAATGATGATGATGTTAGTTGTGGTGTTGATGATGGTAATGATAATGATTGTGATGATGGTGGTGGTGGTGGTGATGATGGTGATG, SVLEN=485, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:38653053 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr20:38653054-38653283, CTG_NAMES=[asm028418:tig00000], END=38653053, MAPPING_QUALITIES=46,28, MAX_ALIGN_LENGTH=1478, SVLEN=259, SVTYPE=INS} GT=[] filters=, [VC null @ chr20:38653283 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={CPX_EVENT=CPX_chr20:38653054-38653283, CTG_NAMES=[asm028418:tig00000], END=38653283, MAPPING_QUALITIES=46,28, MAX_ALIGN_LENGTH=1478, SVLEN=175, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[12]([VC null @ chr20:23122561-23122996 Q. of type=SYMBOLIC alleles=[C*, <CPX>] attr={ALT_ARRANGEMENT=1,2,-1, CTG_NAMES=asm028059:tig00000,asm028059:tig00001, END=23122996, MAPPING_QUALITIES=30,24,7, MAX_ALIGN_LENGTH=593, SEGMENTS=chr20:23122561-23122596,chr20:23122596-23122666,chr20:23122666-23122996, SEQ_ALT_HAPLOTYPE=CTGTCATGTCACCGTGTGGGAGGGCTTGCAGGTGAAGTGGTCTGGGAGGGGTCCCCCAGACAAAGCCAAGGTTCTGAGAGTTGGCCCGAACACTGCTGGATTCCACTTCACCTGCAAGCCCTCCCACACGGTGACATGACAGC, SVLEN=-293, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:23122666-23122995 Q. of type=SYMBOLIC alleles=[C*, <DEL>] attr={CPX_EVENT=CPX_chr20:23122561-23122996, CTG_NAMES=[asm028059:tig00000, asm028059:tig00001], END=23122995, MAPPING_QUALITIES=30,24,7, MAX_ALIGN_LENGTH=593, SVLEN=-329, SVTYPE=DEL} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[13]([VC null @ chr20:34732145-34733344 Q. of type=SYMBOLIC alleles=[G*, <CPX>] attr={ALT_ARRANGEMENT=-3,-2,UINS-14,3, CTG_NAMES=asm010456:tig00000, END=34733344, MAPPING_QUALITIES=53,20, MAX_ALIGN_LENGTH=1358, SEGMENTS=chr20:34732145-34733303,chr20:34733303-34733342,chr20:34733342-34733344, SEQ_ALT_HAPLOTYPE=GTTGTCCAGGTGGATCTTGAGTATTTTTAGTAGAGACGGGGGGTTCAATTAACTCTTCCAA, SVLEN=-1139, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:34732145-34733302 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={CPX_EVENT=CPX_chr20:34732145-34733344, CTG_NAMES=[asm010456:tig00000], END=34733302, MAPPING_QUALITIES=53,20, MAX_ALIGN_LENGTH=1358, SVLEN=-1157, SVTYPE=DEL} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[14]([VC null @ chr21:26001843-26002386 Q. of type=SYMBOLIC alleles=[A*, <CPX>] attr={ALT_ARRANGEMENT=-1, CTG_NAMES=asm029075:tig00000, END=26002386, MAPPING_QUALITIES=55,15, MAX_ALIGN_LENGTH=3677, SEGMENTS=chr21:26001844-26002384,chr21:26002384-26002386, SEQ_ALT_HAPLOTYPE=ACAATGTCAATACAAATGGGGACTAACTATTGTTTTACTTCCCTATACACGTTGCTCTTTCAGTAGATGCAATAAAGTACTGGTAAAACCAGAGGTGGCTACCATCACGATGATGTCAACAGGAGGGACAGTCAGCACTAAGCCCAGAAGGTGTCAAACACTCCGCAGGAGAAATGCGCCATGCAACGGACATGAAGATGATCTGACACTCTTCACGTGGTTTTCAGATGGAAACGTGGCTACGAAAGCATCAACCTCATTATCATCCATCATTAAGGCCATCTCACTCAGTACTGCTGCTTTCAAAGTCCACGCTCCCAAAGCAAATTGGATTTCTGTACACAATACTCTTACAGGATGAAACCCAACCAACTTGTTGACGTAAGTATCCCATCTACTTCGCAATTTTATTTATCTTCCAAAATTAAAGGACTGGCACCCTGATTTATTAAAAGTGAATTGGTTCTAGGGACCATATCCCCTCTGAGTTACTGACAGAGCAGCTTCTGGCCTGTGAAGCTCAAAGCCATGCCTAGATGTGAG, SVLEN=-1, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr21:26001843-26002384 Q. of type=SYMBOLIC alleles=[T*, <INV>] attr={CPX_EVENT=CPX_chr21:26001843-26002386, CTG_NAMES=[asm029075:tig00000], END=26002384, MAPPING_QUALITIES=55,15, MAX_ALIGN_LENGTH=3677, SVLEN=0, SVTYPE=INV} GT=[] filters=]) |
0s |
passed |
| testSegmentedCpxVariantExtractor[15]([VC null @ chr21:23428920-23429023 Q. of type=SYMBOLIC alleles=[T*, <CPX>] attr={ALT_ARRANGEMENT=UINS-84,2,3,UINS-5,2,2,3, CTG_NAMES=asm029052:tig00000,asm029052:tig00001, END=23429023, MAPPING_QUALITIES=26,46,55, MAX_ALIGN_LENGTH=3346, SEGMENTS=chr21:23428920-23428968,chr21:23428968-23428998,chr21:23428998-23429023, SEQ_ALT_HAPLOTYPE=TATAAATATATATAATAATATATAATTATATATTATATTATATAATATAATAATATATATTATAATACATTATATAATATATTATAATATATATAATATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATATTATATAATATATATTACATAATATATTATAT, SVLEN=131, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr21:23428920 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={CPX_EVENT=CPX_chr21:23428920-23429023, CTG_NAMES=[asm029052:tig00000, asm029052:tig00001], END=23428920, MAPPING_QUALITIES=26,46,55, MAX_ALIGN_LENGTH=3346, SVLEN=85, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[16]([VC null @ chr20:13062977-13063278 Q. of type=SYMBOLIC alleles=[C*, <CPX>] attr={ALT_ARRANGEMENT=1,-2,-1,UINS-14, CTG_NAMES=asm016524:tig00000, END=13063278, MAPPING_QUALITIES=56,29, MAX_ALIGN_LENGTH=2885, SEGMENTS=chr20:13062977-13063037,chr20:13063037-13063272,chr20:13063272-13063278, SEQ_ALT_HAPLOTYPE=CTGACCAATCAGCACCCTTGGCTCACTGGCTTACCGATTTCATCTCTGACCAATCAGCACTACTTGCCCACTGCCTAGACAGAGCTGATAAATCAAGACAGGGGAACTGCAATAGAGAAAGAGTAATTCACACAGAGCCGGCTGTGTGGGAGACCAGGGTTTTGTTATTACTCAAATCAGTCTCCCCGAACATTCGGGGAGCAAAGTTTTTAAAAATAACTTGGTGGGTGGGGGGTAAGCCAGTGAGCCAGGAGTGCTGATTGGTCAGAGATGAAATTGGTAAGCCAGTGATCCAGGAGTGCTGATTGGTCAGAGATGAAATCGGTAAGCCAGTGAGCCAGGAGTGCTGATTGGTCAGCACCCTTGGTAACCAC, SVLEN=72, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:13063036-13063272 Q. of type=SYMBOLIC alleles=[G*, <INV>] attr={CPX_EVENT=CPX_chr20:13062977-13063278, CTG_NAMES=[asm016524:tig00000], END=13063272, MAPPING_QUALITIES=56,29, MAX_ALIGN_LENGTH=2885, SVLEN=0, SVTYPE=INV} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[17]([VC null @ chr21:36680290-36680686 Q. of type=SYMBOLIC alleles=[T*, <CPX>] attr={ALT_ARRANGEMENT=1,2,1,UINS-249, CTG_NAMES=asm029759:tig00000,asm029759:tig00001, END=36680686, MAPPING_QUALITIES=7,58,25, MAX_ALIGN_LENGTH=3487, SEGMENTS=chr21:36680290-36680331,chr21:36680331-36680659,chr21:36680659-36680686, SEQ_ALT_HAPLOTYPE=TTCATGATCACTGCCACCTGCATCATGGCTATAATTACCACCGCCATCACCATCATCACTACCACCATCATCACCATCATCACCATTACCACCACCATCACTGCCACCATCACTACCACCATCATCACCATCATCACCACCACCACCATCACCACCATCACCATCACCACTTTCATCACCACCATCTTTATCACAGTCATTATTACCACCATCAATCATCACCACCTTCATGATCACTGCCACCTGCATCATGGTTACAATTACTACCACCACCATCAGCACCACCTTCATGATCACCACCACCTGCATCATGGCTATAATTACTACCACCATCACCACCACTAACACCACCATCATTATCACCACCATCTTCATGATCACTGCCACCTGCATCATGGCTATAATTACCACCATCATCACCACTATACTACCACCACCATCACCACAACCATCGCTACCACCACCACCACCACCATCACCATCATCACCATCACTACTACTGCCACCACTACCAAAACCACCACCACCACCATCACCACCACCATTGCCACCACTACCATCACCACCATCACCACCATCACCATCACCACCACTACCACCATTACCACCACCACCACCACCACCACCACCATCACCACCACCACCACCATCATCACCACTATC, SVLEN=318, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr21:36680686 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr21:36680290-36680686, CTG_NAMES=[asm029759:tig00000, asm029759:tig00001], END=36680686, MAPPING_QUALITIES=7,58,25, MAX_ALIGN_LENGTH=3487, SVLEN=250, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[18]([VC null @ chr20:8888822-8895655 Q. of type=SYMBOLIC alleles=[G*, <CPX>] attr={ALT_ARRANGEMENT=UINS-297,2,UINS-280, CTG_NAMES=asm026939:tig00007, END=8895655, MAPPING_QUALITIES=36,27, MAX_ALIGN_LENGTH=1909, SEGMENTS=chr20:8888822-8895288,chr20:8895288-8895361,chr20:8895361-8895655, SEQ_ALT_HAPLOTYPE=GTTTAGAGGGTCAAGGCGGTGAGTGCAGATGGTGTCCACGCCGGTGGCTGCCCCACGTTTTTCAGGCCTGAGGAGGATAAGTGAGGGGAATGACAATAAGTGGATTGCCTAGGAAGAGGTCCTGAGATTCCTGAGGGAAGGACAGGCAGGGGCCAGAGGAAGTGGTACAGAGGTGAGAAGCTACACATAGATTCTGTGAGTGCACCAACTCCCAGCCAGCCTGGGTCTATGAGCAGAATCATGGACACAAAAATATTTGTAACATTATAAAGTGGATCCTCTGTTCTCAGAAGATGGGGACAGGAGAGCTCAGACTTGAGACAGGTGAAGAGCTGGAATTGGGGATCAAAGCAAGTGGATGAGGCATGTTTGTGTTTGAAAGAAATGCTGGTTGTAGAGTTTATTATCTGCAGGAAAGGGAGGTGGTGGGAAAGGAGGGAACTTAGAGGGATGACCAGGGTAGGGGCCCTATCCTGCTGATGAGCTCTGCAGCATCACTGTTGAGTGGAGAGATGTTACTATCAGGGACACTTTGGTCCTGGAGCCACTGCCTCCTGGATTCCACCAGTGCTGAGGGCACCCCTAGGGAGGGCAGGAAGGAAGTTTTCCAAACTTCTTGGGACTGGGAACAATTGGAGAAGGTAGGCTGGCTCCT, SVLEN=-6179, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr20:8888822-8895287 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={CPX_EVENT=CPX_chr20:8888822-8895655, CTG_NAMES=[asm026939:tig00007], END=8895287, MAPPING_QUALITIES=36,27, MAX_ALIGN_LENGTH=1909, SVLEN=-6465, SVTYPE=DEL} GT=[] filters=, [VC null @ chr20:8895361-8895654 Q. of type=SYMBOLIC alleles=[T*, <DEL>] attr={CPX_EVENT=CPX_chr20:8888822-8895655, CTG_NAMES=[asm026939:tig00007], END=8895654, MAPPING_QUALITIES=36,27, MAX_ALIGN_LENGTH=1909, SVLEN=-293, SVTYPE=DEL} GT=[] filters=, [VC null @ chr20:8888822 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={CPX_EVENT=CPX_chr20:8888822-8895655, CTG_NAMES=[asm026939:tig00007], END=8888822, MAPPING_QUALITIES=36,27, MAX_ALIGN_LENGTH=1909, SVLEN=298, SVTYPE=INS} GT=[] filters=, [VC null @ chr20:8895655 Q. of type=SYMBOLIC alleles=[C*, <INS>] attr={CPX_EVENT=CPX_chr20:8888822-8895655, CTG_NAMES=[asm026939:tig00007], END=8895655, MAPPING_QUALITIES=36,27, MAX_ALIGN_LENGTH=1909, SVLEN=281, SVTYPE=INS} GT=[] filters=]) |
0.002s |
passed |
| testSegmentedCpxVariantExtractor[1]([VC null @ chr21:402806-402905 Q. of type=SYMBOLIC alleles=[GAGTCTTACTCTATTGGGCAGGCTGGAGTACAGCGGTGAAATCATGGCTCACTGCAGCCTCGATGTCCTGGCCTCAAACCATCCCCCTGCTTCAGCCTCC*, <CPX>] attr={ALT_ARRANGEMENT=-1, CTG_NAMES=asm002252:tig00003, END=402905, MAPPING_QUALITIES=9,27, MAX_ALIGN_LENGTH=570, SEGMENTS=chr21:402807-402904, SEQ_ALT_HAPLOTYPE=GAGGCTGAAGCAGGGGGATGGTTTGAGGCCAGGACATCGAGGCTGCAGTGAGCCATGATTTCACCGCTGTACTCCAGCCTGCCCAATAGAGTAAGACT, SVLEN=0, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr21:402806-402904 Q. of type=SYMBOLIC alleles=[N*, <INV>] attr={CPX_EVENT=CPX_chr21:402806-402905, CTG_NAMES=asm002252:tig00003, END=402904, MAPPING_QUALITIES=9,27, MAX_ALIGN_LENGTH=570, SVLEN=0, SVTYPE=INV} GT=[] filters=]) |
0.002s |
passed |
| testSegmentedCpxVariantExtractor[2]([VC null @ chr21:402806-402905 Q. of type=SYMBOLIC alleles=[GAGTCTTACTCTATTGGGCAGGCTGGAGTACAGCGGTGAAATCATGGCTCACTGCAGCCTCGATGTCCTGGCCTCAAACCATCCCCCTGCTTCAGCCTCC*, <CPX>] attr={ALT_ARRANGEMENT=UINS-24,1,UINS-25, CTG_NAMES=asm002252:tig00003, END=402905, MAPPING_QUALITIES=10,53, MAX_ALIGN_LENGTH=3264, SEGMENTS=chr21:402807-402904, SEQ_ALT_HAPLOTYPE=AAAAAAAAAAAAAAAAAAAAAAAAGAGTCTTACTCTATTGGGCAGGCTGGAGTACAGCGGTGAAATCATGGCTCACTGCAGCCTCGATGTCCTGGCCTCAAACCATCCCCCTGCTTCAGCCTCCAAAAAAAAAAAAAAAAAAAAAAAAA, SVLEN=0, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, []) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[3]([VC null @ chr20:18675721-18675877 Q. of type=SYMBOLIC alleles=[TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGT*, <CPX>] attr={ALT_ARRANGEMENT=1,UINS-28,1,UINS-64,1, CTG_NAMES=asm028012:tig00004, END=18675877, MAPPING_QUALITIES=50,7, MAX_ALIGN_LENGTH=1593, SEGMENTS=chr20:18675721-18675877, SEQ_ALT_HAPLOTYPE=TATGTGTATATTTACACACATATATATGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACACATATATATGTGTAAATATACCTATGTGTATATTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCGATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTATGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTGTAAATATACCTATGTGTGTGTTTACACATATATATGTAAATATACCTATGTGT, SVLEN=408, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:18675720 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr20:18675721-18675877, CTG_NAMES=asm028012:tig00004, END=18675720, MAPPING_QUALITIES=50,7, MAX_ALIGN_LENGTH=1593, SVLEN=408, SVTYPE=INS} GT=[] filters=]) |
0.003s |
passed |
| testSegmentedCpxVariantExtractor[4]([VC null @ chr20:64096905-64097041 Q. of type=SYMBOLIC alleles=[CCACCATCATCACCATCACCACTATCACCACCACCACCATCATTACCATCATCATCACGACCATCACCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACC*, <CPX>] attr={ALT_ARRANGEMENT=1,1,UINS-166, CTG_NAMES=asm028821:tig00001, END=64097041, MAPPING_QUALITIES=13,9, MAX_ALIGN_LENGTH=190, SEGMENTS=chr20:64096905-64097041, SEQ_ALT_HAPLOTYPE=CCACCATCATCACCATCACCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACTGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAGTCATCACCGCCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACCATCATCACAATCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACCACCATCATCACCATCACTATCATCACAGTCATCACCGTCACCATCATCACCATCCTCACTATCACCACCACTACCATCATCATCACATTCATCATCACTATTACCATCATCATCACCACCATCACCATCACTATCACCACCATCATTACATTTGTCACCATCACCACCATTATCACCATCACCGCTATCACCACCACCACCGTC, SVLEN=318, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:64097041 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr20:64096905-64097041, CTG_NAMES=asm028821:tig00001, END=64097041, MAPPING_QUALITIES=13,9, MAX_ALIGN_LENGTH=190, SVLEN=318, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[5]([VC null @ chr20:51740560-51741035 Q. of type=SYMBOLIC alleles=[ATTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATT*, <CPX>] attr={ALT_ARRANGEMENT=-chr18:11642876-11642927,UINS-496,1,UINS-49, CTG_NAMES=asm028558:tig00000,asm028558:tig00001, END=51741035, MAPPING_QUALITIES=26,60,54, MAX_ALIGN_LENGTH=1311, SEGMENTS=chr20:51740561-51741034, SEQ_ALT_HAPLOTYPE=AATTAGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGCCTAACCAACATGAGGAAACCCCGTCTCTACTAAAAATACAAAATTAGATGGGCGTGGTGGCGCATGCCTGTAATTCAAACTACTTGGAAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGAGACAGAGGTTGTGGTAAGCCAAGATCATGCCATTGTACTCCAGCATGGGCAACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAATTAGCCAGGCGTGGTGGTGGGCACCTGTAATCCCAGCTACCCTGGAGACTGAGGCAGAAGAATCGCTTGAACCCAGGAGGCGGAGATTGCAGTGAGCCAAGATTACGCCACTGCACTCCAGCCTGGGCACCAAGAGCAAAACCCTGTCTCAAAAAAATTAACAAATAAAAAGATTTCTGTCTGCCACACGGCTGGTCCATGTGTAAAGACACATTCCTGTTGGTTTTATGTGTCTTGAATTCTAATGGGTTTTGTGTTGTTGTTTTTGTTTTTTGAGACAAGGTCTCATTCTGTCACCCAGGCAGGACTGTGGTGGCACCATCATGGCTCAGCGCAGCCTCCTTTTCCCCAGGCTCAAGTGATCCTCTTGCCTCAGCCTCCCACGTGGCTGGGACTACAGGTGTGTACCACCACTCCCGGATAATTTTTTTTATTTTTTATTTTTAGTAAAGACAGTCTCACTATGTTGCCCAGGCTGGTCTCCAACTCCTGGTCTCAAGCAATCCTCCCAGTTCAGCCTCTCAAAGTGCTGGGATTACAGATGTGAGCCACAATACCCGGCCCCAATTCTAATGTTTAAAGAGTACAGTCTACACCTTAAAGCCTGCATTTTATCATCCTGTCCTCACTGCTCTGACTTCTTTACAGTTGTGCTGTCCACCTTGGCGGCTTCTACCACATGTGGCTATTTTAAGTTTCAATTAATTAAAATTAAATTTTAATTTAATTAATTAAAAATAAATTTTAATTAATTAATTAAAAATAAATTTTAAT, SVLEN=599, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:51740560 Q. of type=SYMBOLIC alleles=[A*, <INS>] attr={CPX_EVENT=CPX_chr20:51740560-51741035, CTG_NAMES=asm028558:tig00000,asm028558:tig00001, END=51740560, MAPPING_QUALITIES=26,60,54, MAX_ALIGN_LENGTH=1311, SVLEN=549, SVTYPE=INS} GT=[] filters=, [VC null @ chr20:51741034 Q. of type=SYMBOLIC alleles=[T*, <INS>] attr={CPX_EVENT=CPX_chr20:51740560-51741035, CTG_NAMES=asm028558:tig00000,asm028558:tig00001, END=51741034, MAPPING_QUALITIES=26,60,54, MAX_ALIGN_LENGTH=1311, SVLEN=50, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[6]([VC null @ chr20:20269131-20269199 Q. of type=SYMBOLIC alleles=[ATATATATATATATATACACACACACACACACACATACATATATGTATATACACACACATATATACATA*, <CPX>] attr={ALT_ARRANGEMENT=-chrX:137700299-137700331, CTG_NAMES=asm028026:tig00000, END=20269199, MAPPING_QUALITIES=16,57, MAX_ALIGN_LENGTH=1299, SEGMENTS=chr20:20269131-20269199, SEQ_ALT_HAPLOTYPE=ACACACACACACACACACACACACACACACACACA, SVLEN=-34, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:20269131-20269198 Q. of type=SYMBOLIC alleles=[A*, <DEL>] attr={CPX_EVENT=CPX_chr20:20269131-20269199, CTG_NAMES=asm028026:tig00000, END=20269198, MAPPING_QUALITIES=16,57, MAX_ALIGN_LENGTH=1299, SVLEN=-67, SVTYPE=DEL} GT=[] filters=]) |
0.001s |
passed |
| testSegmentedCpxVariantExtractor[7]([VC null @ chr20:54849491-54849615 Q. of type=SYMBOLIC alleles=[CAAATCTCATGTGAAATGTATCCCCAGTGTGGAGGGGGCAGATCCTCATAATGGCTTGGGCCCTTCCATGGTAATAGTGAGTCTTGCTCTGTAGTTCATAGAGAGCTGATTGTTAAAGGAGTCTG*, <CPX>] attr={ALT_ARRANGEMENT=UINS-36,-chr14:58474127-58474172,UINS-54, CTG_NAMES=asm028586:tig00000, END=54849615, MAPPING_QUALITIES=60,6, MAX_ALIGN_LENGTH=3303, SEGMENTS=chr20:54849491-54849615, SEQ_ALT_HAPLOTYPE=CCAAATCTCATGTTGAAATGTAATCCCCAGTGTTGGAGGGGGGCAGATCCCTCATGAATGGCTTGGTGCCCTTCCCATGGTAATGAGTGAGTTCTTGCTCTGTTAGTTCATGAGAGAGCTGATTGTTTAAAGGAGTCTGG, SVLEN=15, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:54849491-54849614 Q. of type=SYMBOLIC alleles=[C*, <DEL>] attr={CPX_EVENT=CPX_chr20:54849491-54849615, CTG_NAMES=asm028586:tig00000, END=54849614, MAPPING_QUALITIES=60,6, MAX_ALIGN_LENGTH=3303, SVLEN=-123, SVTYPE=DEL} GT=[] filters=, [VC null @ chr20:54849491 Q. of type=SYMBOLIC alleles=[C*, <INS>] attr={CPX_EVENT=CPX_chr20:54849491-54849615, CTG_NAMES=asm028586:tig00000, END=54849491, MAPPING_QUALITIES=60,6, MAX_ALIGN_LENGTH=3303, SVLEN=140, SVTYPE=INS} GT=[] filters=]) |
0s |
passed |
| testSegmentedCpxVariantExtractor[8]([VC null @ chr20:12558793-12558810 Q. of type=SYMBOLIC alleles=[AAAAAAAAAAAAAAAAAA*, <CPX>] attr={ALT_ARRANGEMENT=-chrX:99014092-99014129,UINS-101, CTG_NAMES=asm027960:tig00003, END=12558810, MAPPING_QUALITIES=28,4, MAX_ALIGN_LENGTH=801, SEGMENTS=chr20:12558793-12558810, SEQ_ALT_HAPLOTYPE=AGACAAAGAAACAAACAAACAAAACAAAACTATATATATATATATATACACACACACACACACACACACATTATTAAAATTCAGATTTAAATAAACTGACTATAAAAAAGTACTTTTGAAACAAAAACTTTAATCATGATTATATATATTA, SVLEN=133, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$ZeroAndOneSegmentCpxVariantExtractor@3eb022c2, [[VC null @ chr20:12558793-12558809 Q. of type=SYMBOLIC alleles=[AAAAAAAAAAAAAAAAA*, <INS>] attr={CPX_EVENT=CPX_chr20:12558793-12558810, CTG_NAMES=asm027960:tig00003, END=12558809, MAPPING_QUALITIES=28,4, MAX_ALIGN_LENGTH=801, SVLEN=133, SVTYPE=INS} GT=[] filters=]) |
0s |
passed |
| testSegmentedCpxVariantExtractor[9]([VC null @ chr21:21264944-21265096 Q. of type=SYMBOLIC alleles=[T*, <CPX>] attr={ALT_ARRANGEMENT=1,2,3,2,1,2,3, CTG_NAMES=asm029034:tig00000,asm029034:tig00001, END=21265096, MAPPING_QUALITIES=19,46,19, MAX_ALIGN_LENGTH=3956, SEGMENTS=chr21:21264944-21264988,chr21:21264988-21265052,chr21:21265052-21265096, SEQ_ALT_HAPLOTYPE=TATATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATGTGTATATATATACACATATATATTATATATGTGTATATGTATATATACACATATATATTATATATATATGTGTCTGTATATATATACACATATATATTATATATATGTGTCTGTGTATATATATACACATATATATGTGTCTGTGTATATATGTACACATATATACTATATATGTGTATGTGTATATATATACACACATATATTATATAT, SVLEN=215, SVTYPE=CPX} GT=[] filters=, org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource@246c2f56, org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor$MultiSegmentsCpxVariantExtractor@4dc9e3ea, [[VC null @ chr21:21264943 Q. of type=SYMBOLIC alleles=[G*, <INS>] attr={CPX_EVENT=CPX_chr21:21264944-21265096, CTG_NAMES=[asm029034:tig00000, asm029034:tig00001], END=21264943, MAPPING_QUALITIES=19,46,19, MAX_ALIGN_LENGTH=3956, SVLEN=221, SVTYPE=INS} GT=[] filters=]) |
0.001s |
passed |