All File Changes

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

• 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/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c
  • lines changed 12, context: html, text, full: html, text
    Making a meaningful usage message.
    
• src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c
  • lines changed 4, context: html, text, full: html, text
    Making -dry option produce some output to stdout.
    
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 9, context: html, text, full: html, text
    Dealing with strings longer than 255 characters in tag values.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 39, context: html, text, full: html, text
    Adding a basic validataor for tab separated files and applying it to validate kallisto_abundance
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Adding kallisto_abundance format.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 4, context: html, text, full: html, text
    Making this include a file it depends on.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 11, context: html, text, full: html, text
    Adding eight new tags and a new SRA_ prefix for unchecked tags from the short read archive.
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 69, context: html, text, full: html, text
    A program that adds meta data to a .json file, used for CIRM things
    
  • lines changed 36, context: html, text, full: html, text
    Finishing touches on this program, refs #16182
    
• src/hg/cirm/cdw/wrangle/addMetaDataToJson/makefile
  • lines changed 6, context: html, text, full: html, text
    A program that adds meta data to a .json file, used for CIRM things
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix
  • lines changed 99, context: html, text, full: html, text
    A program that condenses matrices, used for CIRM things. refs #16182
    
  • lines changed 42, context: html, text, full: html, text
    Finishing touches on this program, refs #16182
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/makefile
  • lines changed 6, context: html, text, full: html, text
    A program that condenses matrices, used for CIRM things. refs #16182
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix
  • lines changed 70, context: html, text, full: html, text
    Added in tempfile and cleaned the code up a bit. A new option as well ,refs #16182
    
  • lines changed 170, context: html, text, full: html, text
    Moved this program into its own directory and adding the makefile
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix/makeExpMatrix
  • lines changed 172, context: html, text, full: html, text
    Moved this program into its own directory and adding the makefile
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix/makefile
  • lines changed 6, context: html, text, full: html, text
    Moved this program into its own directory and adding the makefile
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 25, context: html, text, full: html, text
    Adding sub_tissue field from Spyro's spreadsheet.
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 86, context: html, text, full: html, text
    Changed the .html output file, removed some of the unecessary code and split it apart into more fprintf statements
    
• src/hg/hgBlat/hgBlat.c
  • lines changed 8, context: html, text, full: html, text
    adding link back from BLAT results to browser and also
    add a link to the FAQ. refs #16173
    
  • lines changed 4, 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/hgFileSearch/hgFileSearch.c
  • lines changed 10, 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
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• 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/hgTables/correlate.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTables/correlatePlot.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTables/filterFields.c
  • lines changed 13, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    fix after code review, refs #16195
    
• src/hg/hgTables/joining.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• 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/hgTrackUi/encodePeakUi.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• 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/hgTracks/altGraphXTrack.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/bedGraph.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 17, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 70, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 59, context: html, text, full: html, text
    removed too much fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 6, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
  • lines changed 3, context: html, text, full: html, text
    Hiram found that bigWig doesn't work when files from local disk
    are allowed in track hubs. Fixed this, adding a new function.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
• src/hg/hgTracks/loweLabTracks.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/mafTrack.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 2, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
• src/hg/hgTracks/retroGene.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/rnaPLFoldTrack.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/sampleTracks.c
  • lines changed 7, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/searchTracks.c
  • lines changed 9, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 7, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 10, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 16, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/variation.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 18, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
  • lines changed 74, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
  • lines changed 1, context: html, text, full: html, text
    oops...left in a printf
    
• 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/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 4, 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
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/hgc.c
  • lines changed 123, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/lowelab.c
  • lines changed 62, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/mafClick.c
  • lines changed 19, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/retroClick.c
  • lines changed 6, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/hgc/rnaFoldClick.c
  • lines changed 2, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• 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/htdocs/FAQ/FAQblat.html
  • lines changed 63, context: html, text, full: html, text
    adding link back from BLAT results to browser and also
    add a link to the FAQ. refs #16173
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 17, context: html, text, full: html, text
    Revert "Revert "adding menu entries under genomes and genome browser, refs #16022""
    
    This reverts commit 006f356d9ec06729b2693cfeda849e5a6c67c4dd.
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 6, context: html, text, full: html, text
    Revert "Revert "adding menu entries under genomes and genome browser, refs #16022""
    
    This reverts commit 006f356d9ec06729b2693cfeda849e5a6c67c4dd.
    
• src/hg/htdocs/training/index.html
  • lines changed 7, context: html, text, full: html, text
    dropping completed louisville workshop from list
    
• src/hg/inc/customFactory.h
  • lines changed 4, context: html, text, full: html, text
    Hiram found that bigWig doesn't work when files from local disk
    are allowed in track hubs. Fixed this, adding a new function.
    
• src/hg/js/jquery.plugins.js
  • lines changed 1, context: html, text, full: html, text
    Revert "Revert "adding menu entries under genomes and genome browser, refs #16022""
    
    This reverts commit 006f356d9ec06729b2693cfeda849e5a6c67c4dd.
    
• src/hg/lib/customFactory.c
  • lines changed 27, context: html, text, full: html, text
    Hiram found that bigWig doesn't work when files from local disk
    are allowed in track hubs. Fixed this, adding a new function.
    
• src/hg/lib/trackHub.c
  • lines changed 9, context: html, text, full: html, text
    first cut at bigMaf support #15935
    
• src/hg/lib/wikiLink.c
  • lines changed 3, context: html, text, full: html, text
    make wikiLink ready for non-root location, refs #16099
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    Erased allele frequency columns for hg19 and hg38 snp142 tables for rows
    on the '-' strand and with 1000GENOMES among their submitters because they
    contained incorrect values due to a change in how dbSNP copied data from
    SNPAlleleFreq_TGP into SNP_AlleleFreq (they stopped strand-correcting).
    Regenerated snp142{Common,Flagged,Mult} tables since membership in
    Common & Flagged depends on allele frequencies and many of the affected
    variants were mistakenly included in snp142Common. (Bug #16204)
    These changes include a fix from February 2015 (MLQ #14836) that was
    not pushed (updated SNP table restoring ~80M missing 'valid' col values).
    refs #16204, #14836
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 30, context: html, text, full: html, text
    Erased allele frequency columns for hg19 and hg38 snp142 tables for rows
    on the '-' strand and with 1000GENOMES among their submitters because they
    contained incorrect values due to a change in how dbSNP copied data from
    SNPAlleleFreq_TGP into SNP_AlleleFreq (they stopped strand-correcting).
    Regenerated snp142{Common,Flagged,Mult} tables since membership in
    Common & Flagged depends on allele frequencies and many of the affected
    variants were mistakenly included in snp142Common. (Bug #16204)
    These changes include a fix from February 2015 (MLQ #14836) that was
    not pushed (updated SNP table restoring ~80M missing 'valid' col values).
    refs #16204, #14836
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding gorGor4 definitions refs #16220
    
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • lines changed 4, context: html, text, full: html, text
    Fixing kind of subtle bug in ordering of indexes in output.
    
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 64, context: html, text, full: html, text
    some repeat browser stuff for David
    
• 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/hg/oneShot/freen/freen.c
  • lines changed 26, context: html, text, full: html, text
    Seeing if an apostrophe in a printf format string adds commas at thousands millions, etd in big numbers in the C library the way it now does in bash. It does not yet work in C.
    
• src/hg/utils/automation/genbank/README.txt
  • lines changed 52, context: html, text, full: html, text
    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
    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
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/cpgDescription.pl
  • lines changed 3, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• 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/gapDescription.pl
  • lines changed 5, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/gatewayPage.pl
  • lines changed 40, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/gc5Description.pl
  • lines changed 12, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/gpToIx.pl
  • lines changed 32, 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
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/hubIndexNcbi.sh
  • lines changed 33, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/idScan.sh
  • lines changed 2, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiGene.sh
  • lines changed 62, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiGeneDescription.pl
  • lines changed 91, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiGroup.sh
  • lines changed 132, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiHtml.sh
  • lines changed 23, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiPartitioned.sh
  • lines changed 195, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/ncbiPartitionedHtml.sh
  • lines changed 108, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• 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/ncbiToUcsc.sh
  • lines changed 76, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/noStructureAgp.pl
  • lines changed 12, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/rmsk.sh
  • 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/rmskDescription.pl
  • lines changed 3, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• src/hg/utils/automation/genbank/trackDb.sh
  • lines changed 19, context: html, text, full: html, text
    updated scripts to manage both genbank and refseq assemblies refs #16078
    
• 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/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
  • lines changed 79, 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/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/utils/makeTableList/makeTableList.c
  • lines changed 17, context: html, text, full: html, text
    adding generic databases to makeTableList -all option, refs #16158
    
• src/hg/xmlToSql/xmlToSql.c
  • lines changed 1, context: html, text, full: html, text
    Adding check to ensure we don't write off the end of the string (and into other memory)
    
  • lines changed 1, context: html, text, full: html, text
    need to aadd assocTableName back into the table hash refs #16191
    
  • lines changed 1, context: html, text, full: html, text
    After discussion with Hiram, removing unnecessary check
    
• src/inc/bbiFile.h
  • lines changed 1, context: html, text, full: html, text
    a tweak to allow bedToBigBed to work with tab separated files and extra
    indices. Bug found by Hiram. No redmine
    
• src/inc/cda.h
  • lines changed 9, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/cheapcgi.h
  • lines changed 7, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/codebias.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/crudeali.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/ens.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/flydna.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/fof.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/fuzzyFind.h
  • lines changed 5, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/gdf.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/gff.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgGene.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgap.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hgdb.h
  • lines changed 6, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/hmmstats.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/keys.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/maDbRep.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/maToFf.h
  • lines changed 10, context: html, text, full: html, text
    Fixing copyright on some old essentially public domain files.
    
• src/inc/memgfx.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/nib.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/nt4.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/oldGff.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/patSpace.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/sig.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/snof.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/snofmake.h
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    Fixing copyright statement.
    
• src/inc/spaceSaver.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/supStitch.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/tagStorm.h
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    Adding tagStormIndexExtended.
    
• src/inc/trans3.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/unfin.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/wormdna.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/xa.h
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    Fixing copyright on some old essentially public domain files.
    
• src/inc/xenalign.h
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    Fixing copyright on some old essentially public domain files.
    
• src/lib/bbiWrite.c
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    a tweak to allow bedToBigBed to work with tab separated files and extra
    indices. Bug found by Hiram. No redmine
    
• src/lib/portimpl.h
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    Fixing copyright on some old essentially public domain files.
    
• src/lib/rqlEval.c
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    Adding error message for evaluation non-integer strings as integers.
    
• src/lib/tagStorm.c
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    Adding tagStormIndexExtended.
    
• src/pyLib/__init__.py
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    Adding in the new python library structure, refs #16156
    
• src/pyLib/common.py
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    Adding in the new python library structure, refs #16156
    
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
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    Revamping code so that fields that are not in lock step, but that are completely predictable based on key field, can be glommed into a stanza. Changing scoring of partitioning to get partial credit in these predictable but not lock step cases. It tends to result in less partitioning into deep nests of one line stanzas until the end.
    
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    Renaming stuff from Locked to Predictable to better reflect new context.
    
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    Improving commenting, removing some debugging code, and clamping a weight to be no more than 1.
    
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    Turning uglyfs to verbose-2's
    
• src/tagStorm/tagStormJoinTab/tagStormJoinTab.c
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    Making it so that it only joins to actual stanza with ID, not child stanzas as well.
    
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    a tweak to allow bedToBigBed to work with tab separated files and extra
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• src/utils/bedToBigBed/bedToBigBed.c
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    a tweak to allow bedToBigBed to work with tab separated files and extra
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• src/utils/ccCp/ccCp.c
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    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/utils/makefile
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    Adding in the new python library structure, refs #16156
    
• src/utils/newPythonProg/newPythonProg.c
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    Adding in the new python library structure, refs #16156
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v324 preview2 refs #16188
    

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