Commits for hiram

v341_preview to v341_preview2 (2016-10-24 to 2016-10-31) v341

63980a0aa8fe0c595e96237f718c67b6e5e7449e Tue Oct 25 10:08:11 2016 -0700

• fix bogus space in Colobus angolensis names refs #18281
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

47935f35970aa966bb3252ea417ada300355687d Tue Oct 25 15:19:53 2016 -0700

• per user request lift to galGal5 refs #18256
  • src/hg/makeDb/doc/galGal3.txt - lines changed 17, context: html, text, full: html, text

983a72ac8888109a38adc922985eb110702d1af0 Wed Oct 26 14:23:12 2016 -0700

• improve usage message refs #13553
  • src/hg/genePredCheck/genePredCheck.c - lines changed 5, context: html, text, full: html, text

15c947622c017bc89c25268e210c9ab9b3223e01 Wed Oct 26 15:53:47 2016 -0700

• fixups to script to work on an assembly hub and fixup URL references refs #13553
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 43, context: html, text, full: html, text

413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700

• text files for mouse strain hub hierarchy refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.description.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.ensGene.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.names.tab - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.description.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.ensGene.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.names.tab - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.description.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.ensGene.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.names.tab - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.description.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.ensGene.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.names.tab - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.description.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.ensGene.html - lines changed 30, context: html, text, full: html, text
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  • src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.trackDb.txt - lines changed 230, context: html, text, full: html, text
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b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700

• catch up scripts that build mouse assembly hub refs #13553
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17927a47ad8a2443fea7fd8e5a78f0e4ffbb89a3 Mon Oct 31 09:48:35 2016 -0700

• add unmaskedSeq argument to work with 2bit files not in any UCSC hierarchy refs #13553
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0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700

• catching up ensGene definitions refs #18240
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8802bb71ea19b0595adf39d63c57d2d6b735c1bb Mon Oct 31 10:03:12 2016 -0700

• v341 preview2 refs #18302
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text