722e46a2cca739fb7abe042315e8ca3c5e55f8f5 braney Wed Sep 23 14:25:15 2026 -0700 Run the hg/utils tests from make test, and fix the two that had gone red, no redmine make test never reached hg/utils. hg/makefile only descends into an app that has a tests/makefile, and hg/utils has none, so the hubCheck, vcfToHgvs and other hg/utils tests were skipped without a message. Added utils to TEST_DIRS. hubCheck stopped warning about a track with no description page after 1258d7f65e7. A track with no page now keeps the empty string that trackDbCustom.c sets, and hubCheck tested for NULL. It now uses isEmpty(). badType gained a real error when 571aecdf42c stopped dropping tracks, and its expected output was never updated. vcfToHgvs stopLoss reads the live hg38 ncbiRefSeq tables, which now have 32 more transcripts and NM_153819.2. diff --git src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab index e49b3ca147d..94f61e91f98 100644 --- src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab +++ src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab @@ -22,29 +22,61 @@ 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_001440690.1 NC_000011.10:g.64727301_64727304delATTA NM_001440690.1:n.1976_1979delTAAT NM_001440690.1:c.1831_*1delTAAT NP_001427619.1:p.Ter611Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440691.1 NC_000011.10:g.64727301_64727304delATTA NM_001440691.1:n.2042_2045delTAAT NM_001440691.1:c.1831_*1delTAAT NP_001427620.1:p.Ter611Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440692.1 NC_000011.10:g.64727301_64727304delATTA NM_001440692.1:n.1987_1990delTAAT NM_001440692.1:c.1831_*1delTAAT NP_001427621.1:p.Ter611Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440693.1 NC_000011.10:g.64727301_64727304delATTA NM_001440693.1:n.2008_2011delTAAT NM_001440693.1:c.1831_*1delTAAT NP_001427622.1:p.Ter611Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440694.1 NC_000011.10:g.64727301_64727304delATTA NM_001440694.1:n.2064_2067delTAAT NM_001440694.1:c.1828_*1delTAAT NP_001427623.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440695.1 NC_000011.10:g.64727301_64727304delATTA NM_001440695.1:n.2005_2008delTAAT NM_001440695.1:c.1828_*1delTAAT NP_001427624.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440696.1 NC_000011.10:g.64727301_64727304delATTA NM_001440696.1:n.2091_2094delTAAT NM_001440696.1:c.1828_*1delTAAT NP_001427625.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440697.1 NC_000011.10:g.64727301_64727304delATTA NM_001440697.1:n.2012_2015delTAAT NM_001440697.1:c.1828_*1delTAAT NP_001427626.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440698.1 NC_000011.10:g.64727301_64727304delATTA NM_001440698.1:n.2089_2092delTAAT NM_001440698.1:c.1828_*1delTAAT NP_001427627.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440699.1 NC_000011.10:g.64727301_64727304delATTA NM_001440699.1:n.2134_2137delTAAT NM_001440699.1:c.1828_*1delTAAT NP_001427628.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440700.1 NC_000011.10:g.64727301_64727304delATTA NM_001440700.1:n.2039_2042delTAAT NM_001440700.1:c.1828_*1delTAAT NP_001427629.1:p.Ter610Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440701.1 NC_000011.10:g.64727301_64727304delATTA NM_001440701.1:n.2036_2039delTAAT NM_001440701.1:c.1825_*1delTAAT NP_001427630.1:p.Ter609Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440702.1 NC_000011.10:g.64727301_64727304delATTA NM_001440702.1:n.1981_1984delTAAT NM_001440702.1:c.1825_*1delTAAT NP_001427631.1:p.Ter609Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440703.1 NC_000011.10:g.64727301_64727304delATTA NM_001440703.1:n.2074_2077delTAAT NM_001440703.1:c.1918_*1delTAAT NP_001427632.1:p.Ter640Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440704.1 NC_000011.10:g.64727301_64727304delATTA NM_001440704.1:n.2126_2129delTAAT NM_001440704.1:c.1915_*1delTAAT NP_001427633.1:p.Ter639Argext*42 +chr11 64727300 NM_001098671:c.1828_1831del TATTA T NM_001440705.1 NC_000011.10:g.64727301_64727304delATTA NM_001440705.1:n.2068_2071delTAAT NM_001440705.1:c.1912_*1delTAAT NP_001427634.1:p.Ter638Argext*42 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 64727300 NM_001098671:c.1828_1831del TATTA T NM_153819.2 NC_000011.10:g.64727301_64727304delATTA NM_153819.2:n.1973_1976delTAAT NM_153819.2: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 chr11 64727304 NM_001098671:c.1828T>A A T NM_001098671.2 NC_000011.10:g.64727304A>T NM_001098671.2:n.2039T>A NM_001098671.2:c.1828T>A NP_001092141.1:p.Ter610Lysext*1 chr11 64727304 NM_001098671:c.1828T>A A T NM_001318398.2 NC_000011.10:g.64727304A>T NM_001318398.2:n.1959T>A NM_001318398.2:c.1393T>A NP_001305327.1:p.Ter465Lysext*1 chr11 64727304 NM_001098671:c.1828T>A A T NM_001376262.1 NC_000011.10:g.64727304A>T NM_001376262.1:n.-4107T>A NM_001376262.1:c.-4578T>A NP_001363191.1:p.? chr11 64727304 NM_001098671:c.1828T>A A T NM_001376263.1 NC_000011.10:g.64727304A>T NM_001376263.1:n.-4107T>A NM_001376263.1:c.-4578T>A NP_001363192.1:p.? chr11 64727304 NM_001098671:c.1828T>A A T NM_001376265.1 NC_000011.10:g.64727304A>T NM_001376265.1:n.-4107T>A NM_001376265.1:c.-4578T>A NP_001363194.1:p.? chr11 64727304 NM_001098671:c.1828T>A A T NM_001376266.1 NC_000011.10:g.64727304A>T NM_001376266.1:n.-4107T>A NM_001376266.1:c.-4578T>A NP_001363195.1:p.? chr11 64727304 NM_001098671:c.1828T>A A T NM_001376267.1 NC_000011.10:g.64727304A>T NM_001376267.1:n.-4107T>A NM_001376267.1:c.-4578T>A NP_001363196.1:p.? +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440690.1 NC_000011.10:g.64727304A>T NM_001440690.1:n.1976T>A NM_001440690.1:c.1831T>A NP_001427619.1:p.Ter611Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440691.1 NC_000011.10:g.64727304A>T NM_001440691.1:n.2042T>A NM_001440691.1:c.1831T>A NP_001427620.1:p.Ter611Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440692.1 NC_000011.10:g.64727304A>T NM_001440692.1:n.1987T>A NM_001440692.1:c.1831T>A NP_001427621.1:p.Ter611Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440693.1 NC_000011.10:g.64727304A>T NM_001440693.1:n.2008T>A NM_001440693.1:c.1831T>A NP_001427622.1:p.Ter611Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440694.1 NC_000011.10:g.64727304A>T NM_001440694.1:n.2064T>A NM_001440694.1:c.1828T>A NP_001427623.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440695.1 NC_000011.10:g.64727304A>T NM_001440695.1:n.2005T>A NM_001440695.1:c.1828T>A NP_001427624.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440696.1 NC_000011.10:g.64727304A>T NM_001440696.1:n.2091T>A NM_001440696.1:c.1828T>A NP_001427625.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440697.1 NC_000011.10:g.64727304A>T NM_001440697.1:n.2012T>A NM_001440697.1:c.1828T>A NP_001427626.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440698.1 NC_000011.10:g.64727304A>T NM_001440698.1:n.2089T>A NM_001440698.1:c.1828T>A NP_001427627.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440699.1 NC_000011.10:g.64727304A>T NM_001440699.1:n.2134T>A NM_001440699.1:c.1828T>A NP_001427628.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440700.1 NC_000011.10:g.64727304A>T NM_001440700.1:n.2039T>A NM_001440700.1:c.1828T>A NP_001427629.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440701.1 NC_000011.10:g.64727304A>T NM_001440701.1:n.2036T>A NM_001440701.1:c.1825T>A NP_001427630.1:p.Ter609Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440702.1 NC_000011.10:g.64727304A>T NM_001440702.1:n.1981T>A NM_001440702.1:c.1825T>A NP_001427631.1:p.Ter609Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440703.1 NC_000011.10:g.64727304A>T NM_001440703.1:n.2074T>A NM_001440703.1:c.1918T>A NP_001427632.1:p.Ter640Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440704.1 NC_000011.10:g.64727304A>T NM_001440704.1:n.2126T>A NM_001440704.1:c.1915T>A NP_001427633.1:p.Ter639Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_001440705.1 NC_000011.10:g.64727304A>T NM_001440705.1:n.2068T>A NM_001440705.1:c.1912T>A NP_001427634.1:p.Ter638Lysext*1 chr11 64727304 NM_001098671:c.1828T>A A T NM_015080.4 NC_000011.10:g.64727304A>T NM_015080.4:n.-4107T>A NM_015080.4:c.-4578T>A NP_055895.1:p.? chr11 64727304 NM_001098671:c.1828T>A A T NM_138732.3 NC_000011.10:g.64727304A>T NM_138732.3:n.-4107T>A NM_138732.3:c.-4578T>A NP_620060.1:p.? -chr11 64727304 NM_001098671:c.1828T>A A T NM_153819.1 NC_000011.10:g.64727304A>T NM_153819.1:n.2081T>A NM_153819.1:c.1828T>A NP_722541.1:p.Ter610Lysext*1 +chr11 64727304 NM_001098671:c.1828T>A A T NM_153819.2 NC_000011.10:g.64727304A>T NM_153819.2:n.1973T>A NM_153819.2:c.1828T>A NP_722541.1:p.Ter610Lysext*1