All File Changes

v322_preview2 to v322_base (2015-09-07 to 2015-09-14) v322

• README
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    adding link to mirror instructions refs #15969
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix
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    A python program that generates an expression matrix from kallisto oututs.
    
• src/hg/cirm/cdw/wrangle/makeFastqManifest
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    A python program that generates a fastqManifest file from meta data files. Was used for the first Quake CIRM submission
    
• src/hg/cirm/cdw/wrangle/makeKallistoManifest
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    A python program that generates a manifestKallisto.txt file from a manifestFastq.txt file. Was used for the first Quake CIRM submission.
    
• src/hg/expMatrixToJson/expData.c
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    removing an outdated program, expData that was renamed ot expMatrixToJson
    
• src/hg/hgCustom/hgCustom.c
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    Oops, forgot to use the previously selected CGI as the form's initial action.
    refs #15517
    
• src/hg/hgSession/hgSession.c
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    Changing wording to hgSessions requested by Bob refs #15971
    
• src/hg/hgTables/hgTables.c
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    If the current table doesn't have hti, getIdField tries to get hti for
    the current track -- except that's a problem when the track is a composite
    track yet has a type for which we expect to have a bigDataFileOrUrl.
    So if the current track is a composite, don't try.
    Test case: Table Browser, hg19, group = Variation, track = 1000G Ph3 Accsbl;
    before fix, page fails trying to query the non-existent table for composite.
    
• src/hg/hgTrackUi/hgTrackUi.c
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    fix crash in snake track controls refs #15994
    
• src/hg/hgTracks/hgTracks.c
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    fixing typo, refs #15113
    
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    making shortcuts work by default and fixing MSIE bugs. refs #15370
    
• src/hg/hgTracks/menu.c
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    typo, refs #15113
    
• src/hg/htdocs/FAQ/FAQlink.html
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    Adding a change to Session link info per Bob input
    
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    Further change to Session link info on FAQlink.html per Bob/Donna input
    
• src/hg/htdocs/goldenPath/newsarch.html
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    Removing release tags related to 100-way and pushing announcement, refs #14560
    
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    Added draft for hg38 default announcement.
    
• src/hg/htdocs/images/phylo/ce11_26way.png
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    phylo tree diagram for ce11 26-way alignment refs #15209
    
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    phylo tree diagram for ce11 26-way alignment refs #15209
    
• src/hg/htdocs/indexNews.html
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    Removing release tags related to 100-way and pushing announcement, refs #14560
    
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    Added draft for hg38 default announcement.
    
• src/hg/inc/hubConnect.h
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    add ability to specify a genome within an assembly hub (no redmine)
    
• src/hg/inc/versionInfo.h
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    New version number v322
    
• src/hg/lib/hubConnect.c
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    add ability to specify a genome within an assembly hub (no redmine)
    
• src/hg/lib/web.c
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    Hooked up hgIntegrator to hgIntegratorHelp.html in menuBar's Help menu (thanks Donna for noticing it was missing!).
    
• src/hg/makeDb/doc/ce11/multiz26way.txt
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    done with frames and 4d tree estimation refs #15209
    
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    done with phastCons and phyloP refs #15209
    
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    done with downloads creation and documentation updated refs #15209
    
• src/hg/makeDb/doc/hg19.txt
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    Reload PeptidAtlas table to fix load problem. refs #15998
    
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    Reload PeptidAtlas table to fix load problem. refs #15998
    
  • lines changed 94, context: html, text, full: html, text
    Re-ran snp144 pipeline after dbSNP re-dumped their mappings to alt haplo sequences
    after Sarah Hunt from EBI noticed that many were missing.
    refs #15493
    
• src/hg/makeDb/doc/hg38/variation.txt
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    Re-ran snp144 pipeline after dbSNP re-dumped their mappings to alt haplo sequences
    after Sarah Hunt from EBI noticed that many were missing.
    refs #15493
    
• src/hg/makeDb/doc/makeEnsembl.txt
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    ensGene v81 released refs #15796
    
• src/hg/makeDb/makefile
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    adding hgLoadChain and hgLoadNet to the utils build refs #15955
    
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    hgLoadMaf and hgLoadMafSummary can be in utils also refs #15955
    
• src/hg/makeDb/schema/all.joiner
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    adding rules for ce11 refs #15209
    
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
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    corrected fr2 ensGene search rules refs #15796
    
• src/hg/makeDb/trackDb/human/hg38/alpha.7way.ra
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    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/betaPublic.7way.ra
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    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
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    clean up 60-way references, change HTML tags to lower case refs #14560
    
  • lines changed 240, context: html, text, full: html, text
    Adding release-tagged trackDb entries to manage release of 100-way hg38 data.Will undo changes at release. refs #14560
    
  • lines changed 240, context: html, text, full: html, text
    Fixing accidental reversion of Hiram's commit f297ad795ccca47069c23da6c892b58e8a3c0ce0
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 9, context: html, text, full: html, text
    Adding release-tagged trackDb entries to manage release of 100-way hg38 data.Will undo changes at release. refs #14560
    
  • lines changed 9, context: html, text, full: html, text
    Removing release tags related to 100-way and pushing announcement, refs #14560
    
  • lines changed 1, context: html, text, full: html, text
    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
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    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
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    Adding release-tagged trackDb entries to manage release of 100-way hg38 data.Will undo changes at release. refs #14560
    
  • lines changed 13, context: html, text, full: html, text
    Removing release tags related to 100-way and pushing announcement, refs #14560
    
  • lines changed 1, context: html, text, full: html, text
    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.7way.ra
  • lines changed 10, context: html, text, full: html, text
    Fixing 100-way shortLabel and adjusting priorities values, refs #14560
    
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
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    description page for 26-way refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.26way.ra
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    setting default viz and configure 26way correctly refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    setting default viz and configure 26way correctly refs #15209
    
• src/hg/utils/automation/doDbSnp.pl
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    Re-ran snp144 pipeline after dbSNP re-dumped their mappings to alt haplo sequences
    after Sarah Hunt from EBI noticed that many were missing.
    refs #15493
    
• src/hg/utils/automation/doDbSnpMaskSequence.pl
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    Re-ran snp144 pipeline after dbSNP re-dumped their mappings to alt haplo sequences
    after Sarah Hunt from EBI noticed that many were missing.
    refs #15493
    
• src/hg/utils/otto/clinvar/clinVarToBed
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    clinvar has changed their format again
    
• src/product/README.mysql.setup
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    further notes on mysql and ssl
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v322 final build refs #15948
    

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• files changed: 57