Commits for hiram

v324_preview to v324_preview2 (2015-10-12 to 2015-10-19) v324

• updated scripts to manage both genbank and refseq assemblies refs #16078
  
  • src/hg/utils/automation/genbank/buildStats.pl - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/cpgDescription.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gapDescription.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gatewayPage.pl - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gc5Description.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gpToIx.pl - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/idScan.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiGene.sh - lines changed 62, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiGeneDescription.pl - lines changed 91, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiToUcsc.sh - lines changed 76, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/noStructureAgp.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rmsk.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/rmskDescription.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/trackDb.sh - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/unlocalizedFasta.pl - lines changed 1, context: html, text, full: html, text
• updated scripts to manage both genbank and refseq assemblies refs #16078
  
  • src/hg/utils/automation/genbank/hubHtml.pl - lines changed 104, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/hubIndexNcbi.sh - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiGroup.sh - lines changed 132, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiHtml.sh - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiPartitioned.sh - lines changed 195, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiPartitionedHtml.sh - lines changed 108, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiPartitionedHubIndexNcbi.sh - lines changed 98, context: html, text, full: html, text
• updated scripts to manage both genbank and refseq assemblies refs #16078
  
  • src/hg/utils/automation/genbank/cpg.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/cronUpdate.sh - lines changed 46, context: html, text, full: html, text
• updated scripts to manage both genbank and refseq assemblies refs #16078
  
  • src/hg/utils/automation/genbank/README.txt - lines changed 52, context: html, text, full: html, text
• need to aadd assocTableName back into the table hash refs #16191
  
  • src/hg/xmlToSql/xmlToSql.c - lines changed 1, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgTracks/altGraphXTrack.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTracks/bedGraph.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/cytoBandTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/expRatioTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 70, context: html, text, full: html, text
  • src/hg/hgTracks/loweLabTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/mafTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/retroGene.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/rmskJoinedTrack.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/rnaPLFoldTrack.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/sampleTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTracks/snakeTrack.c - lines changed 16, context: html, text, full: html, text
  • src/hg/hgTracks/variation.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/wigMafTrack.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c - lines changed 9, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgTracks/snakeTrack.c - lines changed 2, context: html, text, full: html, text
• removed too much fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgTracks/hgTracks.c - lines changed 59, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgc/expClick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 123, context: html, text, full: html, text
  • src/hg/hgc/lowelab.c - lines changed 62, context: html, text, full: html, text
  • src/hg/hgc/mafClick.c - lines changed 19, context: html, text, full: html, text
  • src/hg/hgc/retroClick.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgc/rnaFoldClick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/virusClick.c - lines changed 3, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgTrackUi/encodePeakUi.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 6, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgTables/correlate.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/correlatePlot.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgTables/joining.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c - lines changed 5, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgGene/microarray.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgGene/synonym.c - lines changed 1, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgUserSuggestion/hgUserSuggestion.c - lines changed 4, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgFileSearch/hgFileSearch.c - lines changed 10, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgConvert/hgConvert.c - lines changed 4, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/hgBlat/hgBlat.c - lines changed 4, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/hg/near/hgNear/expRatio.c - lines changed 3, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/aladdin/aladdin/aladdin.c - lines changed 3, context: html, text, full: html, text
• fixup gcc warnings for -Wunused-but-set-variable refs #16121
  
  • src/utils/ccCp/ccCp.c - lines changed 3, context: html, text, full: html, text
• generic construction of chromosome AGP and FASTA files from chr2acc and FASTA and AGP directories in a genbank genome release refs #16220
  
  • src/hg/utils/automation/ucscCompositeAgp.pl - lines changed 62, context: html, text, full: html, text
• generic construction of unlocalized chromosome bits AGP and FASTA files from chr2acc and FASTA and AGP directories in a genbank genome release refs #16220
  
  • src/hg/utils/automation/unlocalizedWithChroms.pl - lines changed 79, context: html, text, full: html, text
• generic construction of unplaced chromosome bits AGP and FASTA files from chr2acc and FASTA and AGP directories in a genbank genome release refs #16220
  
  • src/hg/utils/automation/unplacedWithChroms.pl - lines changed 48, context: html, text, full: html, text
• adding gorGor4 definitions refs #16220
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• v324 preview2 refs #16188
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text