eeda64a71cfc7fe13b91130dcf6e6cdc22767059 galt Thu Mar 30 17:19:13 2023 -0700 Make test was failing for utility vcfToHgvs. The stopLoss for the test NM_005572.3 just picked up more alignments from hg38. Added these to the expected list. diff --git src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab index c7b7c5d..e49b3ca 100644 --- src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab +++ src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab @@ -1,19 +1,40 @@ chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001257374.3 NC_000001.11:g.156134876_156134899delinsCCCC NM_001257374.3:n.409_432delinsCCCC NM_001257374.3:c.375_398delinsCCCC NP_001244303.1:p.Glu126ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001282624.2 NC_000001.11:g.156134876_156134899delinsCCCC NM_001282624.2:n.589_612delinsCCCC NM_001282624.2:c.468_491delinsCCCC NP_001269553.1:p.Glu157ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001282625.2 NC_000001.11:g.156134876_156134899delinsCCCC NM_001282625.2:n.1357_1380delinsCCCC NM_001282625.2:c.711_734delinsCCCC NP_001269554.1:p.Glu238ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001282626.2 NC_000001.11:g.156134876_156134899delinsCCCC NM_001282626.2:n.919_942delinsCCCC NM_001282626.2:c.711_734delinsCCCC NP_001269555.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406983.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406983.1:n.1245_1268delinsCCCC NM_001406983.1:c.711_734delinsCCCC NP_001393912.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406984.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406984.1:n.1245_1268delinsCCCC NM_001406984.1:c.711_734delinsCCCC NP_001393913.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406985.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406985.1:n.919_942delinsCCCC NM_001406985.1:c.711_734delinsCCCC NP_001393914.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406986.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406986.1:n.1099_1122delinsCCCC NM_001406986.1:c.468_491delinsCCCC NP_001393915.1:p.Glu157ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406987.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406987.1:n.589_612delinsCCCC NM_001406987.1:c.468_491delinsCCCC NP_001393916.1:p.Glu157ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406988.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406988.1:n.534_557delinsCCCC NM_001406988.1:c.414_437delinsCCCC NP_001393917.1:p.Glu139ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406989.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406989.1:n.409_432delinsCCCC NM_001406989.1:c.375_398delinsCCCC NP_001393918.1:p.Glu126ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406990.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406990.1:n.762_785delinsCCCC NM_001406990.1:c.153_176delinsCCCC NP_001393919.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406991.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406991.1:n.1025_1048delinsCCCC NM_001406991.1:c.711_734delinsCCCC NP_001393920.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406992.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406992.1:n.1025_1048delinsCCCC NM_001406992.1:c.711_734delinsCCCC NP_001393921.1:p.Glu238ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406993.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406993.1:n.463_486delinsCCCC NM_001406993.1:c.153_176delinsCCCC NP_001393922.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406994.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406994.1:n.919_942delinsCCCC NM_001406994.1:c.47_70delinsCCCC NP_001393923.1:p.Leu16SerfsTer100 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406995.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406995.1:n.762_785delinsCCCC NM_001406995.1:c.153_176delinsCCCC NP_001393924.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406996.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406996.1:n.623_646delinsCCCC NM_001406996.1:c.153_176delinsCCCC NP_001393925.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406997.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406997.1:n.452_475delinsCCCC NM_001406997.1:c.153_176delinsCCCC NP_001393926.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406998.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406998.1:n.409_432delinsCCCC NM_001406998.1:c.375_398delinsCCCC NP_001393927.1:p.Glu126ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001406999.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001406999.1:n.1099_1122delinsCCCC NM_001406999.1:c.47_70delinsCCCC NP_001393928.1:p.Leu16SerfsTer100 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001407000.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001407000.1:n.919_942delinsCCCC NM_001407000.1:c.47_70delinsCCCC NP_001393929.1:p.Leu16SerfsTer100 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001407001.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001407001.1:n.762_785delinsCCCC NM_001407001.1:c.47_70delinsCCCC NP_001393930.1:p.Leu16SerfsTer100 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001407002.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001407002.1:n.1107_1130delinsCCCC NM_001407002.1:c.153_176delinsCCCC NP_001393931.1:p.Glu52ProfsTer9 +chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_001407003.1 NC_000001.11:g.156134876_156134899delinsCCCC NM_001407003.1:n.463_486delinsCCCC NM_001407003.1:c.153_176delinsCCCC NP_001393932.1:p.Glu52ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_005572.4 NC_000001.11:g.156134876_156134899delinsCCCC NM_005572.4:n.919_942delinsCCCC NM_005572.4:c.711_734delinsCCCC NP_005563.1:p.Glu238ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_170707.4 NC_000001.11:g.156134876_156134899delinsCCCC NM_170707.4:n.919_942delinsCCCC NM_170707.4:c.711_734delinsCCCC NP_733821.1:p.Glu238ProfsTer9 chr1 156134875 NM_005572.3:c.711_734delinsCCCC TTGAGAGCCGGCTGGCGGATGCGCT TCCCC NM_170708.4 NC_000001.11:g.156134876_156134899delinsCCCC NM_170708.4:n.919_942delinsCCCC NM_170708.4:c.711_734delinsCCCC NP_733822.1:p.Glu238ProfsTer9 chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001098670.2 NC_000011.10:g.64727301_64727304delATTA NM_001098670.2:n.1984_1987delTAAT NM_001098670.2:c.1828_*1delTAAT NP_001092140.1:p.Ter610Argext*42 chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001098671.2 NC_000011.10:g.64727301_64727304delATTA NM_001098671.2:n.2039_2042delTAAT NM_001098671.2:c.1828_*1delTAAT NP_001092141.1:p.Ter610Argext*42 chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001318398.2 NC_000011.10:g.64727301_64727304delATTA NM_001318398.2:n.1959_1962delTAAT NM_001318398.2:c.1393_*1delTAAT NP_001305327.1:p.Ter465Argext*42 chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001376262.1 NC_000011.10:g.64727301_64727304delATTA NM_001376262.1:n.-4107_-4104delTAAT NM_001376262.1:c.-4578_-4575delTAAT NP_001363191.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001376263.1 NC_000011.10:g.64727301_64727304delATTA NM_001376263.1:n.-4107_-4104delTAAT NM_001376263.1:c.-4578_-4575delTAAT NP_001363192.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001376265.1 NC_000011.10:g.64727301_64727304delATTA NM_001376265.1:n.-4107_-4104delTAAT NM_001376265.1:c.-4578_-4575delTAAT NP_001363194.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001376266.1 NC_000011.10:g.64727301_64727304delATTA NM_001376266.1:n.-4107_-4104delTAAT NM_001376266.1:c.-4578_-4575delTAAT NP_001363195.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001376267.1 NC_000011.10:g.64727301_64727304delATTA NM_001376267.1:n.-4107_-4104delTAAT NM_001376267.1:c.-4578_-4575delTAAT NP_001363196.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_015080.4 NC_000011.10:g.64727301_64727304delATTA NM_015080.4:n.-4107_-4104delTAAT NM_015080.4:c.-4578_-4575delTAAT NP_055895.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_138732.3 NC_000011.10:g.64727301_64727304delATTA NM_138732.3:n.-4107_-4104delTAAT NM_138732.3:c.-4578_-4575delTAAT NP_620060.1:p.? chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_153819.1 NC_000011.10:g.64727301_64727304delATTA NM_153819.1:n.2081_2084delTAAT NM_153819.1:c.1828_*1delTAAT NP_722541.1:p.Ter610Argext*42 chr11 64727304 NM_001098671:c.1828T>A A T NM_001098670.2 NC_000011.10:g.64727304A>T NM_001098670.2:n.1984T>A NM_001098670.2:c.1828T>A NP_001092140.1:p.Ter610Lysext*1