All File Changes

v311_preview2 to v311_base (2015-01-20 to 2015-01-26) v311

• src/hg/encode3/cellsFromEncode3.py
  • lines changed 62, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
• src/hg/hgAi/hgAi.c
  • lines changed 11, context: html, text, full: html, text
    Added header comments as suggested by Kate. refs #14698
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 11, context: html, text, full: html, text
    Added header comments as suggested by Kate. refs #14698
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    Use composite color for dense mode center label (instead of first track
• src/hg/hgTracks/multiWig.c
  • lines changed 2, context: html, text, full: html, text
    force black labels on unaggregated full multiwigs (JK request)
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    Make wigLeftLbels respect color param. Needed to force black labels on unaggregated full multiwigs (JK request)
• src/hg/hgc/peakClusters.c
  • lines changed 51, context: html, text, full: html, text
    Merge duplicated code. refs #14353
  • lines changed 64, context: html, text, full: html, text
    Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353
  • lines changed 10, context: html, text, full: html, text
    Add link to table browser view of table in 'more info' section of clutser details (as we have no metadata link). refs #14353
• src/hg/hgc/retroClick.c
  • lines changed 2, context: html, text, full: html, text
    Changed table heading to match corresponding description section for table. Changed column heading to Score as it is not a percentage, score is from 0-130.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Changing University affiliation on credits per CR, refs #14655
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 1, context: html, text, full: html, text
    realized I had the date wrong for when we released genome-euro. refs #14707
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    changed html quotes, per code review #14704
  • lines changed 15, context: html, text, full: html, text
    unhiding announcement of YouTube channel, making links to channel spawn new window, moved the 2014 tag on newsarch down to proper place below first 2015 entry. refs #12700
  • lines changed 6, context: html, text, full: html, text
    Adding credit to Matt and updating to reference bit.ly links. refs #14525
  • lines changed 7, context: html, text, full: html, text
    added a line to news item asking for suggestions for vids.
• src/hg/htdocs/googlef42dd384148a3435.html
  • lines changed 1, context: html, text, full: html, text
    Adding verification file to associate youtube account with our website. refs #14525
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    changed html quotes, per code review #14704
  • lines changed 5, context: html, text, full: html, text
    unhiding announcement of YouTube channel, making links to channel spawn new window, moved the 2014 tag on newsarch down to proper place below first 2015 entry. refs #12700
  • lines changed 6, context: html, text, full: html, text
    Adding credit to Matt and updating to reference bit.ly links. refs #14525
  • lines changed 7, context: html, text, full: html, text
    added a line to news item asking for suggestions for vids.
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    removed individual vidXX.html pages from vids dir. fixed pointers on training/index.html page to point to internal anchors on vids/index.html page. refs #12700
  • lines changed 2, context: html, text, full: html, text
    fixed link to YouTube channel to go directly to video page. refs
  • lines changed 2, context: html, text, full: html, text
    Swapping out link for bit.ly link to monitor traffic. refs #14525
• src/hg/htdocs/training/vids/index.html
  • lines changed 7, context: html, text, full: html, text
    added Page Index title to vid/index.html page. refs #14525
  • lines changed 3, context: html, text, full: html, text
    Correcting times to match durations posted on youtube. Refs #14525
• src/hg/htdocs/training/vids/vid01.html
  • lines changed 66, context: html, text, full: html, text
    removed individual vidXX.html pages from vids dir. fixed pointers on training/index.html page to point to internal anchors on vids/index.html page. refs #12700
• src/hg/htdocs/training/vids/vid02.html
  • lines changed 63, context: html, text, full: html, text
    removed individual vidXX.html pages from vids dir. fixed pointers on training/index.html page to point to internal anchors on vids/index.html page. refs #12700
• src/hg/htdocs/training/vids/vid03.html
  • lines changed 66, context: html, text, full: html, text
    removed individual vidXX.html pages from vids dir. fixed pointers on training/index.html page to point to internal anchors on vids/index.html page. refs #12700
• src/hg/htdocs/training/vids/vid04.html
  • lines changed 69, context: html, text, full: html, text
    removed individual vidXX.html pages from vids dir. fixed pointers on training/index.html page to point to internal anchors on vids/index.html page. refs #12700
• src/hg/inc/encode/wgEncodeCell.h
  • lines changed 2, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
• src/hg/inc/hui.h
  • lines changed 10, context: html, text, full: html, text
    Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v311
• src/hg/js/README
  • lines changed 53, context: html, text, full: html, text
    Adding new UI framework big commit comment as suggested by Kate. refs #14698
• src/hg/js/install.mk
  • lines changed 1, context: html, text, full: html, text
    Fixing typo caught by Galt. refs #14666
• src/hg/js/utils.js
  • lines changed 16, context: html, text, full: html, text
    Fix table sort bug (wasn't doing subsorts on columns other than the clicked one). refs #14723
• src/hg/lib/encode/wgEncodeCell.as
  • lines changed 1, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
• src/hg/lib/encode/wgEncodeCell.c
  • lines changed 18, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
• src/hg/lib/encode/wgEncodeCell.sql
  • lines changed 1, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
• src/hg/lib/hui.c
  • lines changed 86, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
  • lines changed 47, context: html, text, full: html, text
    Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353
  • lines changed 1, context: html, text, full: html, text
    Fix typo caught by alert Angie during review.
  • lines changed 2, context: html, text, full: html, text
    fixing reload bug, refs #14561
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Use color constant (one step toward using style)
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 440, context: html, text, full: html, text
    initial build in progress refs #14017
• src/hg/makeDb/doc/danRer10/ucscCompositeAgp.pl
  • lines changed 62, context: html, text, full: html, text
    initial build in progress refs #14017
• src/hg/makeDb/doc/danRer10/unplaced.pl
  • lines changed 48, context: html, text, full: html, text
    initial build in progress refs #14017
• src/hg/makeDb/doc/dm6.txt
  • lines changed 63, context: html, text, full: html, text
    from user request liftover to dm3 refs #14794
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 127, context: html, text, full: html, text
    Documented building the Retroposed Genes V9 track.
• src/hg/makeDb/doc/hg38/hg38Patch2.txt
  • lines changed 23, context: html, text, full: html, text
    fixup off by one error in the hg38 loaded tracks refs #14167
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 6, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
  • lines changed 19, context: html, text, full: html, text
    Add link to table browser view of table in 'more info' section of clutser details (as we have no metadata link). refs #14353
• src/hg/makeDb/doc/hg38/regionScan.pl
  • lines changed 1, context: html, text, full: html, text
    fixup off by one error in the hg38 loaded tracks refs #14167
• src/hg/makeDb/doc/mm10.txt
  • lines changed 76, context: html, text, full: html, text
    adding lastz chain net to sheep oviAri3 refs #14625
  • lines changed 133, context: html, text, full: html, text
    Documented building the Retroposed Genes V6 track.
  • lines changed 2, context: html, text, full: html, text
    Corrected typos in Retroposed Genes V6 documentation.
  • lines changed 2, context: html, text, full: html, text
    added more information to the Retroposed Genes V6 track.
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 26, context: html, text, full: html, text
    alignment pig to sheep refs #14625
  • lines changed 24, context: html, text, full: html, text
    adding lastz chain net to sheep oviAri3 refs #14625
• src/hg/makeDb/doc/proteins/150115.txt
  • lines changed 213, context: html, text, full: html, text
    proteins, uniprot, and a start to ucsc genes.
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 79, context: html, text, full: html, text
    alignment to sheep refs #14625
  • lines changed 1, context: html, text, full: html, text
    alignment pig to sheep refs #14625
• src/hg/makeDb/doc/tarSyr2/multiz17way.txt
  • lines changed 116, context: html, text, full: html, text
    finish downloads and in the pushQ refs #13560
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.csh
  • lines changed 1629, context: html, text, full: html, text
    proteins, uniprot, and a start to ucsc genes.
• src/hg/makeDb/doc/uniProt/sp150115.txt
  • lines changed 92, context: html, text, full: html, text
    proteins, uniprot, and a start to ucsc genes.
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added macFas5 - crab-eating macaque refs #11174
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added macFas5 - crab-eating macaque refs #11174
• src/hg/makeDb/schema/all.joiner
  • lines changed 33, context: html, text, full: html, text
    Added snp*ExceptionDesc for versions starting with 132 (#3606). Added snp142 (#14189).refs #3606 #14189
    
  • lines changed 21, context: html, text, full: html, text
    Added Retroposed Genes V6 for mm10 (ucscRetro*6) and Retroposed Genes V9 for hg38 (ucscRetro*9).
  • lines changed 11, context: html, text, full: html, text
    adding felCat8 refs #14412
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • lines changed 38, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 82, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/chicken/galGal3/phastConsElements7way.html
  • lines changed 50, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • lines changed 13, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
  • lines changed 9, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroAna2.html
  • lines changed 23, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroEre1.html
  • lines changed 26, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/chainDroYak2.html
  • lines changed 33, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevSignal.html
  • lines changed 33, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/affyDrosDevTransfrags.html
  • lines changed 33, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/bacEndPairs.html
  • lines changed 7, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 71, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/nscanPasaGene.html
  • lines changed 38, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/phastConsElements15way.html
  • lines changed 45, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/dm3/pscreen.html
  • lines changed 18, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/evofold.html
  • lines changed 1, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/geneMapper.html
  • lines changed 1, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/netDp3.html
  • lines changed 1, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroAna2.html
  • lines changed 21, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroEre1.html
  • lines changed 20, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/drosophila/netDroYak2.html
  • lines changed 21, context: html, text, full: html, text
    Updating links and references on D melanogaster (dm3) track description pages
• src/hg/makeDb/trackDb/gwipsvizRiboseq.html
  • lines changed 2, context: html, text, full: html, text
    Fixed Ingolia (2014) in-text citation - only one author on that particular paper; refs #14066
• src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on hedgehog (eriEur1) track description pages
• src/hg/makeDb/trackDb/hedgehog/eriEur1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on hedgehog (eriEur1) track description pages
• src/hg/makeDb/trackDb/hedgehog/eriEur1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on hedgehog (eriEur1) track description pages
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 53, context: html, text, full: html, text
    Added track for and searches for Retroposed Genes V9.
  • lines changed 1, context: html, text, full: html, text
    added dataVersion line for ucscRetroAli6.
• src/hg/makeDb/trackDb/human/hg38/ucscRetroAli9.html
  • lines changed 146, context: html, text, full: html, text
    Description for Retroposed Genes V9 track.
  • lines changed 1, context: html, text, full: html, text
    Edited track description.
  • lines changed 1, context: html, text, full: html, text
    Added tag so that link from Break in Orthology table will jump to the text in this description describing that feature.
  • lines changed 14, context: html, text, full: html, text
    Updated description as per Robert Baertsch's suggestions. Corrected reference to assembly.
• src/hg/makeDb/trackDb/human/hg38/uwDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
  • lines changed 5, context: html, text, full: html, text
    Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353
  • lines changed 191, context: html, text, full: html, text
    Add link to table browser view of table in 'more info' section of clutser details (as we have no metadata link). refs #14353
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on anoCar2, choHof1, echTel1, melGal1, and taeGut1 gateway pages
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    initial files for danRer10 refs #14017
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on marmoset (calJac1) track description pages
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 53, context: html, text, full: html, text
    Added track and searches for Retroposed Genes V6.
  • lines changed 1, context: html, text, full: html, text
    added dataVersion line for ucscRetroAli6.
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli6.html
  • lines changed 146, context: html, text, full: html, text
    Description for Retroposed Genes V6 track.
  • lines changed 1, context: html, text, full: html, text
    Edited track description.
  • lines changed 1, context: html, text, full: html, text
    Added tag so that link from Break in Orthology table will jump to the text in this description describing that feature.
  • lines changed 13, context: html, text, full: html, text
    Updated description as per Robert Baertsch's suggestions.
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
  • lines changed 34, context: html, text, full: html, text
    Updating mouse Gencode Supertrack description page
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.ra
  • lines changed 1, context: html, text, full: html, text
    Making Gencode VM3 hideen by default, refs #14529
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on yeast (sacCer3) track description pages
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on yeast (sacCer3) track description pages
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on anoCar2, choHof1, echTel1, melGal1, and taeGut1 gateway pages
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Add 'subGroupMetaTables' setting to trackDb. This setting allows specification of a metadata table (minimally description+url) describing terms in a subgroup (e.g. hgFixed.wgEncodeCell for the 'cellType' subgroup in ENCODE tracks. This ia aimed at providing basic metadata functionality with lower overhead than the cv.ra + metaDb table used during ENCODE2. refs #14353
  • lines changed 1, context: html, text, full: html, text
    Add inputFieldMetaTables setting to trackDb. It provides a way to add meta tables to non-composites (same functionality as subGroupMetaTables setting). Used in details of DNase clusters, to replace cv.ra and metaDb. refs #14353
• src/hg/makeDb/trackDb/tenrec/echTel1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on anoCar2, choHof1, echTel1, melGal1, and taeGut1 gateway pages
• src/hg/makeDb/trackDb/transMap.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/transMapAlnMRna.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/transMapAlnRefSeq.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on chicken (galGal3 and galGal4) track description pages
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on anoCar2, choHof1, echTel1, melGal1, and taeGut1 gateway pages
• src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html
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    catch up with config.ra files refs #14560
• src/hg/utils/automation/configFiles/speTri1.config.ra
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• src/hg/utils/automation/configFiles/strPur3.config.ra
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• src/hg/utils/automation/configFiles/strPur4.config.ra
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• src/hg/utils/automation/configFiles/sudEbo1.config.ra
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• src/hg/utils/automation/configFiles/susScr1.config.ra
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• src/hg/utils/automation/configFiles/susScr2.config.ra
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• src/hg/utils/automation/configFiles/taeGut1.config.ra
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• src/hg/utils/automation/configFiles/taeGut2.config.ra
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• src/hg/utils/automation/configFiles/taiEbo1.config.ra
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• src/hg/utils/automation/configFiles/tarSyr2.config.ra
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• src/hg/utils/automation/configFiles/tetNig2.config.ra
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• src/hg/utils/automation/configFiles/tupBel1.config.ra
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• src/hg/utils/automation/configFiles/turTru1.config.ra
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• src/hg/utils/automation/configFiles/vicPac2.config.ra
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• src/hg/utils/automation/configFiles/vicVic1.config.ra
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• src/hg/utils/automation/configFiles/xenTro3.config.ra
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• src/hg/utils/automation/configFiles/xenTro7.config.ra
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• src/hg/utils/automation/configFiles/zaiEbo1.config.ra
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• src/hg/utils/automation/doBlastzChainNet.pl
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    correct symlink for synNet downloads refs #14560
• src/hg/utils/automation/ucscToINSDC.sh
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    this has matured to a generic point now, see make danRer10 doc for usage procedure refs #14017
• src/lib/asParse.c
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    Added a check for duplicate column names in .as autoSql table definition used by big* and other utilities. This will also catch accidentally duplicated lines in an editor. Check for unique column names is case-insensitive which is also what myqsl does.
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    fix a bug in asParse.c:mustFindColumn where column was not returned.
• src/utils/git-reports/git-reports.c
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    Omit react/bundle/ files from git reports; they are generated from *.jsx files,but included in git so that mirror sites don't need to install node & react
    tools. Also, don't suppress any newlines in the git commit message. The code
    was intended to suppress the final newline but it was suppressing the first.
    refs #14698
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v311 final build refs #14648

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