All File Changes

v301_preview2 to v301_base (2014-06-02 to 2014-06-09) v301

• src/ai/paraFlow/compiler/pfToken.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/ai/paraFlow/runtime/argsEnv.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/ai/paraFlow/runtime/runErr.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/ameme/ameme.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/blatz/client.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/blatz/server.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/blatz/standalone.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/aliGlue/aliGlue.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/c2gCheck/g2cCheck.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/exonAli/exonAli.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/g2cCheck/g2cCheck.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/patSpace/findHits.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/patSpace/glueBacs.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/patSpace/patSpace.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/cdnaAli/refineAli/refineAli.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/fuzzyFind/ffapp.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/gfServer/gfServer.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/altSplice/altSplice/altPaths.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/altSplice/altSplice/altSplice.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/altSplice/exonWalk/exonWalk.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/autoSql/autoSql.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/autoSql/tests/jsonTest.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/checkTableCoords/checkTableCoords.c
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    I found that checkTableCoords.c was skipping hg38 tables (doh!) becauseit bailed on databases with too many sequences to have split tables --
    formerly those were only the huge scaffold-based databases. For now,
    to cover hg38 with minimal change, I have increased the number of assembly
    sequences to query independently from 100 to 1000. In the longer term it
    would be better to rewrite this to use whole-table query so it could
    support all assemblies.
    
• src/hg/ctgToChromFa/ctgToChromFa.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode/encodePatchTdb/encodePatchTdb.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode/lib/encodePatchTdb.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/eap/eapDaemon/eapDaemon.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
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    Restricting scheduling to output of previous step for now.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
  • lines changed 55, context: html, text, full: html, text
    Adding support for bed_ formats to warehouse.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
  • lines changed 59, context: html, text, full: html, text
    Adding support for bed_ formats to warehouse.
• src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/edwRsyncEdwUser/edwRsyncEdwUser.c
  • lines changed 7, context: html, text, full: html, text
    encode3 RM Specifications 1264:1. Change url from "http://submit.encodedcc.org"
    to "https://www.encodedcc.org"
    2. Add one more parameter to access the email address of
    a user such as:
    https://www.encodedcc.org/users/4d07ff68-9372-407c-8479-ad3709a7e917/?format=json&datastore=database
    
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
  • lines changed 22, context: html, text, full: html, text
    Adding support for bed_ formats to warehouse.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 4, context: html, text, full: html, text
    Adding support for bed_ formats to warehouse.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
  • lines changed 15, context: html, text, full: html, text
    Adding support for bed_ formats to warehouse.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 44, context: html, text, full: html, text
    Dealing with changes in Stanford URLs. Making biosample getter cache
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 4, context: html, text, full: html, text
    Dealing with changes in Stanford URLs. Making biosample getter cache
• src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c
  • lines changed 2, context: html, text, full: html, text
    Bumping version to 2.
• src/hg/encode3/encodeDataWarehouse/utils/edwClusterMethylBed/edwClusterMethylBed.c
  • lines changed 231, context: html, text, full: html, text
    renamed analyzeCpG to edwClusterMethylBed, added some comments, and fixed a few bugs
• src/hg/encode3/encodeDataWarehouse/utils/edwClusterMethylBed/makefile
  • lines changed 3, context: html, text, full: html, text
    renamed analyzeCpG to edwClusterMethylBed, added some comments, and fixed a few bugs
• src/hg/encode3/encodeDataWarehouse/utils/makefile
  • lines changed 11, context: html, text, full: html, text
    If USE_BAM is not set, don't compile encodeDataWarehouse utils that require samtools.
• src/hg/encode3/validateManifest/VERSION.TXT
  • lines changed 1, context: html, text, full: html, text
    closing vm 1.9 to new features so we can get it released
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 61, context: html, text, full: html, text
    Changing to use encode3BedType library shared by warehouse and validators.
• src/hg/extractPslForLfs/extractPslForLfs.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/fqToQa/fqToQa.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/fqToQac/fqToQac.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/genePredToMrna/genePredToMrna.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/cmParse/cmParse.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/gapper/gapper.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/mendMap/mendMap.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/mm/mm/mm.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/ooGreedy/bak/ooGreedy.39.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/ooGreedy/bak/ooGreedy.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/ooGreedy/ooGreedy.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/gigAssembler/psLayout/psLayout.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgConvert/hgConvert.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgCoordConv/hgCoordConv.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 4, context: html, text, full: html, text
    change "Delete Search Terms" to "Select All Hubs", add styles for theConnect and Disconnect buttons.
    
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
  • lines changed 46, context: html, text, full: html, text
    some hgHubConnect clean ups
  • lines changed 11, context: html, text, full: html, text
    some polishing of text. Make "disconnect" return to hgHubConnect
  • lines changed 1, context: html, text, full: html, text
    tweak label in hgHubConnect
  • lines changed 7, context: html, text, full: html, text
    oops... another tweak to get "no public hubs" message to come out
• src/hg/hgLiftOver/hgLiftOver.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgPcr/hgPcr.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgTracks/renderMain.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgc/lowelab.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/hgc/retroClick.c
  • lines changed 11, context: html, text, full: html, text
    Added code to handle casewhere there is no version number for the retrogene id instead of reporting an error.
  • lines changed 1, context: html, text, full: html, text
    Removed extra word from error message.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Switch ENCODE home page Visualization link to an hg19 session
• src/hg/htdocs/images/Drosophila_melanogaster.jpg
  • lines changed 0, context: html, text, full: html, text
    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/htdocs/images/phylo/hg38_7way.png
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    phylo tree for hg38 7way refs #13300
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    change "Delete Search Terms" to "Select All Hubs", add styles for theConnect and Disconnect buttons.
    
  • lines changed 10, context: html, text, full: html, text
    some hgHubConnect clean ups
• src/hg/inc/cart.h
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/inc/encode3/encode3Valid.h
  • lines changed 17, context: html, text, full: html, text
    Added encode3BedType structure and a table of these so that there is hopefully just one place where we store info about the as files we accept for ENCODE.
• src/hg/inc/hPrint.h
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    some hgHubConnect clean ups
• src/hg/inc/versionInfo.h
  • lines changed 4, context: html, text, full: html, text
    New version number v301
• src/hg/inc/wiggle.h
  • lines changed 1, context: html, text, full: html, text
    add negateValues trackDb variable
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/encode3/encode3Valid.c
  • lines changed 34, context: html, text, full: html, text
    Added encode3BedType structure and a table of these so that there is hopefully just one place where we store info about the as files we accept for ENCODE.
• src/hg/lib/findKGAlias.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/findKGProtAlias.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/hCommon.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/hgExp.c
  • lines changed 1, context: html, text, full: html, text
    Looking for NULL as well as 'null'
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/loweutils.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/lib/wiggleCart.c
  • lines changed 5, context: html, text, full: html, text
    add negateValues trackDb variable
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 1, context: html, text, full: html, text
    Reloading tracks with reformatted IDs refs #10954
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    Including script used to figure out regex for trackDb search settings for animal QTL tracks. refs #10954
• src/hg/makeDb/doc/dm6.txt
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    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 50, context: html, text, full: html, text
    Including script used to figure out regex for trackDb search settings for animal QTL tracks. refs #10954
• src/hg/makeDb/doc/hg38.txt
  • lines changed 283, context: html, text, full: html, text
    initial 7-way alignment completed refs #13300
  • lines changed 235, context: html, text, full: html, text
    annotation and frames added to 7-way refs #13300
  • lines changed 117, context: html, text, full: html, text
    completed 4D 7-way prediction refs #13300
  • lines changed 649, context: html, text, full: html, text
    completed 7-way alignment refs #13300
  • lines changed 110, context: html, text, full: html, text
    alignment downloads constructed for the 7-way refs #13300
• src/hg/makeDb/doc/mm10.txt
  • lines changed 12, context: html, text, full: html, text
    Adding makedoc entries for FaceBase microarray track. refs #12606
• src/hg/makeDb/doc/mm9.txt
  • lines changed 14, context: html, text, full: html, text
    Adding makedoc entries for FaceBase microarray track. refs #12606
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 17, context: html, text, full: html, text
    Reloading tracks with reformatted IDs refs #10954
  • lines changed 50, context: html, text, full: html, text
    Including script used to figure out regex for trackDb search settings for animal QTL tracks. refs #10954
• src/hg/makeDb/doc/rn5.txt
  • lines changed 28, context: html, text, full: html, text
    add wiki pages for rn5 13-way refs #8212
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 3, context: html, text, full: html, text
    Reloading tracks with reformatted IDs refs #10954
  • lines changed 48, context: html, text, full: html, text
    Including script used to figure out regex for trackDb search settings for animal QTL tracks. refs #10954
• src/hg/makeDb/genbank/src/dbload/gbAlignData.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/gbSanity/metaData.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbAligned.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbFa.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbFileOps.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbPipeline.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbProcessed.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbStatusTbl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/gbVerb.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/lib/sqlUpdater.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/process/gbProcess.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/src/selectWithPsl/selectWithPsl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/genbank/tests/subset/gbGetTestSubset.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/hgTraceInfo/hgTraceInfo.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/makeDb/trackDb/animalQtl.html
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    Adding line to description page for sheep. refs #10954
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
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    Fixing url to external description pages - to be compatible with new IDs. refs #10954
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
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    Fixing url to external description pages - to be compatible with new IDs. refs #10954
• src/hg/makeDb/trackDb/drosophila/dm6/description.html
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    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/makeDb/trackDb/drosophila/dm6/gap.html
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    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/makeDb/trackDb/drosophila/dm6/gold.html
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    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
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    Initial works for Assembly #4049 dm6 - fly - D. melanogaster genome release 6
• src/hg/makeDb/trackDb/human/grcIncidentDb.html
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    human incidents now come from a different directory refs #12407
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    moved segmental dups track from variation to repeats group, refs #13355
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
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    initial contents 7way description refs #13300
• src/hg/makeDb/trackDb/human/hg38/trackDb.7way.ra
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    turning on 7-way conservation track refs #13300
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    turning on 7-way conservation track refs #13300
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    moved self chain track from variation to repeats group, refs #13355
• src/hg/makeDb/trackDb/human/trackDb.ra
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    moved self chain track from varation to repeats group, refs #13355
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
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    Adding description page for facebase track refs #12606
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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    Fixing url to external description pages - to be compatible with new IDs. refs #10954
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    Fixing codon translation table typo. refs #8212
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    Adding rat to codon translation table. refs #8212
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    Updating references on rat conservation page, refs #8212
• src/hg/makeDb/trackDb/rat/rn5/cons13way.ra
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    Adding species groups to rat multiz13way. refs #8212
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    Fixing issue with rn5 appearing twice in codon dropdown. refs #8212
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
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    Fixing url to external description pages - to be compatible with new IDs. refs #10954
• src/hg/makeDb/trackDb/tagTypes.tab
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    add negateValues trackDb variable
• src/hg/makeDb/trackDb/trackDb.ra
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    Fixing search rule to work for weird QTL Ids. refs #10954
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    moved segmental dups track from variation to repeats group
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    undoing previous commit
• src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/testCart/cart.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/oneShot/tryGtexBoxPlot/tryGtexBoxPlot.c
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    Upgraded command line so can select from one of three graph types and also several options.
• src/hg/orthoMap/orthoMap.c
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    Mac OS X Mavericks gcc -Wall complained about double-parens in an if statementand mixing of int * (bed) and unsigned int * (genePred).
    
• src/hg/phyloGif/phyloGif.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/ratStuff/mafAddIRows/mafAddIRows.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/ratStuff/mafFilter/mafFilter.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/ratStuff/mafOrder/mafOrder.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/ratStuff/mafToAnc/mafToAnc.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/ratStuff/stageMultiz/stageMultiz.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/rtdbWebUpdate/rtdbWebUpdate.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/snp/details/dbSnp.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/snp/pbToAlleleCounts/pbToAlleleCounts.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/snp/tajD/tajD.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/snpException/snpException.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/spideyToPsl/spideyToPsl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/splignToPsl/splignToPsl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/utils/automation/doBlastzChainNet.pl
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    correctly remove symlink before making perhaps a new one refs #13300
• src/hg/utils/automation/makeGenomeDb.pl
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    updated list of top-level trackDb files to enable the make of trackDb refs #13300
• src/hg/utils/tdbQuery/tdbQuery.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/visiGene/vgPrepImage/jp2Dec.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/hg/zfishBacClonesandSts/zfishBacClonesandSts.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/idbQuery/idbQuery.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/inc/common.mk
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    correct finding libraries on Mavericks with homebrew mysql install refs #12209
• src/inc/errAbort.h
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/inc/errCatch.h
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    Inside an errCatch block warnings which are not followed by an errAbort just get swallowed up and ignored. I added a flag to the structure that remembers that warnings have occurred.
• src/inc/errabort.h
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/isPcr/webPcr/webPcr.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/jkOwnLib/fuzzyFind.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/jkOwnLib/genoFind.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/jkOwnLib/gfBlatLib.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/jkOwnLib/gfInternal.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/kehayden/linearSat/linearSat.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/annoGratorQuery.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/annoStreamer.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/bwgCreate.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/cheapcgi.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/common.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/errAbort.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/errCatch.c
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    Inside an errCatch block warnings which are not followed by an errAbort just get swallowed up and ignored. I added a flag to the structure that remembers that warnings have occurred.
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/errabort.c
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    Inside an errCatch block warnings which are not followed by an errAbort just get swallowed up and ignored. I added a flag to the structure that remembers that warnings have occurred.
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/fa.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/gfNet.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/gff3.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/hmac.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/hmmPfamParse.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/htmlPage.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/htmshell.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/https.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/jointalign.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/linefile.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/log.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/maf.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/makefile
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/meta.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/mime.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/net.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/paraFetch.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/pipeline.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/pthreadWrap.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/qa.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/rudp.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/seg.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/snofmake.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/tests/mimeDecodeTest.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/tests/udcTest.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/textOut.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/tokenizer.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/trix.c
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    fix seeking problem in trix
• src/lib/vcf.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/vcfBits.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/xap.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/lib/xp.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/lib/paraLib.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/lib/paraMessage.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/para/para.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/paraHub/heartbeat.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/paraHub/paraHub.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/parasol/paraNode/paraNode.c
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• src/parasol/parasol/parasol.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/analyzeCpG/analyzeCpG.c
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    renamed analyzeCpG to edwClusterMethylBed, added some comments, and fixed a few bugs
• src/utils/analyzeCpG/makefile
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    renamed analyzeCpG to edwClusterMethylBed, added some comments, and fixed a few bugs
• src/utils/bigWigCat/bigWigCat.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/catDir/catDir.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/est2genomeToPsl/est2genomeToPsl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/fastaToPsl/fastaToPsl.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/git-reports/git-reports.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/htmlCheck/htmlCheck.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/utils/qa/weeklybld/buildEnv.csh
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    v301 final build refs #13189
• src/utils/qa/weeklybld/downloadBuildSettings.mk
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    can have USE_SSL=0 to avoid some lib links in the blat build refs #13189
• src/utils/verticalSplitSqlTable/verticalSplitSqlTable.c
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    Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
• src/webBlat/webBlat.c
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• lines changed: 5340
• files changed: 262