All File Changes

v288_preview to v288_preview2 (2013-08-07 to 2013-08-13) v288

• README
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    a do nothing change to test git push
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    a do nothing change to test git push
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c
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    Little fixer seems to work.
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile
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    Little fixer seems to work.
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c
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    Seems to work. Has run on about 1/3 of ENCODE2.
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    Making it so it only does work if it hasn't done it already.
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    Adding keepTemp command line option. Getting sample from already downsampled file in edwFastqFile table.
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/makefile
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    Seems to work. Has run on about 1/3 of ENCODE2.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
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    Making it call external fastqStatsAndSubsample program. Allowing 'unknown' format files to get license plate.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
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    Allowing mm10 as a ucscDb.
• src/hg/encode3/encodeDataWarehouse/inc/edwFastqFileFromRa.h
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    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
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    Adding support routines for edwFastqFiles.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
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    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c
  • lines changed 305, context: html, text, full: html, text
    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
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    Adding support routines for edwFastqFiles.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
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    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
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    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 49, context: html, text, full: html, text
    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
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    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/lib/redoSchema
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    Moving code generated .h file _before_ the compile!
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
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    Moving it back from hive to scratch while hive is being delicate. Adding e. coli contamination target.
• src/hg/encode3/encodeDataWarehouse/makefile
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    Adding new edwMakeContaminationQa program to build.
• src/hg/hgLogin/hgLogin.c
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    proper handling of username cgi encoding in url
• src/hg/hgTracks/bamTrack.c
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    For BAM custom tracks, base-coloring trackDb settings were automatically set,but that didn't take care of hub tracks, and not all native BAM tracks added
    those settings in their trackDb entries. So, as I should have done from the
    beginning, I'm forcing the base-coloring settings directly in bamMethods.
    fixes #11479
    
• src/hg/hgTracks/hgTracks.c
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    For BAM custom tracks, base-coloring trackDb settings were automatically set,but that didn't take care of hub tracks, and not all native BAM tracks added
    those settings in their trackDb entries. So, as I should have done from the
    beginning, I'm forcing the base-coloring settings directly in bamMethods.
    fixes #11479
    
• src/hg/hgTracks/joinedRmskTrack.c
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    fixup to eliminate globals, passing data in tg structure refs #9741 #11384
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    fixup function declaration format to match kent style refs #11384
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    best use of slAddList refs #11384
• src/hg/htdocs/ENCODE/FAQ/index.html
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    Correcting FAQ link, adding Updated Date to ENCODE FAQ
• src/hg/htdocs/contacts.html
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    updated mailing list archives links to point to Google Groups
• src/hg/htdocs/goldenPath/pubs.html
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    Fixing some previous edits to pubs page, now include full author list for those redone with getTrackReferences, refs #11410
• src/hg/htdocs/training.html
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    updated mailing list archives link to point to Google Groups
• src/hg/lib/mdb.c
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    Further changes to streamline queries due to mysql 5.6 inefficiencies. Redmine #11155. This has been tested on hgwdev-tdreszer.sdsc.edu browser, which is 5.6. However, RR way still be a problem, given cache interference.
• src/hg/makeDb/doc/allMis1.txt
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    fixup search rule for the gold table refs #8750
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    add lastz swap documentation refs #10272
• src/hg/makeDb/doc/echTel2.txt
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    fixup search rule refs #9693
• src/hg/makeDb/doc/musFur1.txt
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    fixup gold table search rule refs #6352
• src/hg/makeDb/doc/oviAri3.txt
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    fixup gold table search rule refs #9409
• src/hg/makeDb/doc/vicPac2.txt
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    fixup search rule for gold table refs #10833
• src/hg/makeDb/genbank/etc/euronode-copy
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    use hgwdev.sdsc for euronode copies
• src/hg/makeDb/genbank/etc/euronode-dbload
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    move to hgwdev.sdsc.edu
• src/hg/makeDb/schema/all.joiner
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    removed duplicate table entry in an identifier
• src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra
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    fixup search rule for gold table refs #10833
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
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    Added the before presence in second sentence to make sentence flow better, refs #8533
• src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra
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    fixup gold table search rule refs #6352
• src/hg/makeDb/trackDb/gator/trackDb.ra
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    fixup search rule for gold track refs #8750
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
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    Adding small changes to V3 TFBS clusters track.html refs# 10097
• src/hg/makeDb/trackDb/human/trackDb.ra
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    Capitalized the 'V' in 'HGMD Variants' short label (redmine #10935)
• src/hg/makeDb/trackDb/makefile
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    no trix for kids refs #8132
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
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    fixup gold table search rule refs #9409
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
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    fixup search rule refs #9693
• src/hg/sqlEnvTest.sh
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    source tree now functioning in new environment in hgwdev.sdsc refs #8875
• src/hg/utils/cpAndLinkToResourceFiles.pl
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    recognize host hgwdevSD refs #8875
• src/hg/utils/phyloTrees/111way.commonNames.nh
  • lines changed 111, context: html, text, full: html, text
    adding strCam1 Ostrich refs #10272
• src/hg/utils/phyloTrees/111way.nh
  • lines changed 111, context: html, text, full: html, text
    adding strCam1 Ostrich refs #10272
• src/hg/utils/phyloTrees/111way.scientificNames.nh
  • lines changed 111, context: html, text, full: html, text
    adding strCam1 Ostrich refs #10272
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
  • lines changed 16, context: html, text, full: html, text
    rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
  • lines changed 76, context: html, text, full: html, text
    rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
  • lines changed 16, context: html, text, full: html, text
    rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
• src/hg/utils/phyloTrees/benchMark100.sh
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    rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
  • lines changed 2, context: html, text, full: html, text
    rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
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    adding strCam1 Ostrich refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    adding strCam1 Ostrich refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding strCam1 Ostrich refs #10272
• src/inc/common.mk
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    source tree now functioning in new environment in hgwdev.sdsc refs #8875
• src/inc/raToStruct.h
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    Added basesInSample output.
• src/lib/hash.c
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    Improving comment.
• src/lib/linefile.c
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    Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
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    Removing weak attempt at fix that Mark properly fixed.
• src/lib/makefile
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    Making raToStruct.c module compile.
• src/lib/pipeline.c
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    Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
• src/lib/raToStruct.c
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    Added basesInSample output.
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    Making raToStruct.c module compile.
• src/userApps/README
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    add note about MySQL access refs #9149
• src/utils/faUniqify/faUniqify.c
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    Seems to work. Sadly it does change line length.
• src/utils/faUniqify/makefile
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    Seems to work. Sadly it does change line length.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
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    Seems to work.
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    Making it write out '@' line again.
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    Adding smallOk option.
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    Added basesInSample output.
  • lines changed 32, context: html, text, full: html, text
    Making it work ok with /dev/null as fastq output. Fixing an integer overflow bug.
• src/utils/fastqStatsAndSubsample/makefile
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    Seems to work.
• src/utils/qa/qaEnsGenes.csh
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    Made changes suggested in code review to limit loading of .hg.conf.beta to a subshell (redmine #11481)
• src/utils/qa/weeklybld/buildEnv.csh
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    Removed MYSQLLIBS and MYSQLINC as they are now specified in common.mk, refs #8875
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    v288 preview2
• src/utils/qa/weeklybld/doNewReview.csh
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    changes necessary to do preview1
• src/utils/qa/weeklybld/makeStrictBeta.csh
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    eliminate useless cd WEEKLY directory changes refs #8875
• src/utils/qa/weeklybld/makeUserApps.csh
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    eliminate useless cd WEEKLY directory changes refs #8875
• src/utils/qa/weeklybld/tagPreview.csh
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    changes necessary to do preview1
• src/utils/raToStructGen/makefile
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    Main ra parsing function is generate and passes visual inspection. Haven't tried compiling it yet though.
• src/utils/raToStructGen/raToStructGen.c
  • lines changed 261, context: html, text, full: html, text
    Main ra parsing function is generate and passes visual inspection. Haven't tried compiling it yet though.
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    Output now compiles.
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    Making it generate a new function.

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• files changed: 93