File Changes for hiram

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

• src/aladdin/aladdin/aladdin.c
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    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgBlat/hgBlat.c
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• src/hg/hgConvert/hgConvert.c
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• src/hg/hgFileSearch/hgFileSearch.c
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• src/hg/hgGene/microarray.c
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• src/hg/hgGene/synonym.c
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• src/hg/hgTables/correlate.c
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• src/hg/hgTables/correlatePlot.c
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• src/hg/hgTables/filterFields.c
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• src/hg/hgTables/joining.c
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• src/hg/hgTables/wiggle.c
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• src/hg/hgTrackUi/encodePeakUi.c
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• src/hg/hgTrackUi/hgTrackUi.c
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• src/hg/hgTracks/altGraphXTrack.c
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• src/hg/hgTracks/bedGraph.c
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• src/hg/hgTracks/cytoBandTrack.c
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• src/hg/hgTracks/expRatioTracks.c
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• src/hg/hgTracks/hgTracks.c
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    removed too much fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/loweLabTracks.c
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• src/hg/hgTracks/mafTrack.c
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• src/hg/hgTracks/retroGene.c
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• src/hg/hgTracks/rmskJoinedTrack.c
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• src/hg/hgTracks/rnaPLFoldTrack.c
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• src/hg/hgTracks/sampleTracks.c
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• src/hg/hgTracks/searchTracks.c
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• src/hg/hgTracks/simpleTracks.c
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• src/hg/hgTracks/snakeTrack.c
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• src/hg/hgTracks/variation.c
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• src/hg/hgTracks/wigMafTrack.c
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• src/hg/hgTracks/wigTrack.c
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• src/hg/hgUserSuggestion/hgUserSuggestion.c
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• src/hg/hgc/expClick.c
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• src/hg/hgc/hgc.c
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• src/hg/hgc/lowelab.c
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• src/hg/hgc/mafClick.c
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• src/hg/hgc/retroClick.c
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• src/hg/hgc/rnaFoldClick.c
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• src/hg/hgc/virusClick.c
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• src/hg/makeDb/genbank/etc/genbank.conf
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    adding gorGor4 definitions refs #16220
    
• src/hg/near/hgNear/expRatio.c
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    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/utils/automation/genbank/README.txt
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/buildStats.pl
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/cpg.sh
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/cpgDescription.pl
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• src/hg/utils/automation/genbank/cronUpdate.sh
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• src/hg/utils/automation/genbank/gapDescription.pl
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• src/hg/utils/automation/genbank/gatewayPage.pl
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• src/hg/utils/automation/genbank/gc5Description.pl
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• src/hg/utils/automation/genbank/gpToIx.pl
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• src/hg/utils/automation/genbank/hubHtml.pl
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• src/hg/utils/automation/genbank/hubIndexNcbi.sh
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• src/hg/utils/automation/genbank/idScan.sh
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• src/hg/utils/automation/genbank/ncbiGene.sh
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• src/hg/utils/automation/genbank/ncbiGeneDescription.pl
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• src/hg/utils/automation/genbank/ncbiGroup.sh
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• src/hg/utils/automation/genbank/ncbiHtml.sh
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• src/hg/utils/automation/genbank/ncbiPartitioned.sh
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• src/hg/utils/automation/genbank/ncbiPartitionedHtml.sh
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• src/hg/utils/automation/genbank/ncbiPartitionedHubIndexNcbi.sh
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiToUcsc.sh
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/noStructureAgp.pl
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• src/hg/utils/automation/genbank/rmsk.sh
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/rmskDescription.pl
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• src/hg/utils/automation/genbank/trackDb.sh
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/unlocalizedFasta.pl
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    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/ucscCompositeAgp.pl
  • lines changed 62, 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/unlocalizedWithChroms.pl
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    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/unplacedWithChroms.pl
  • lines changed 48, 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/xmlToSql/xmlToSql.c
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    need to aadd assocTableName back into the table hash refs #16191
    
• src/utils/ccCp/ccCp.c
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    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v324 preview2 refs #16188