All File Changes

v321_base to v322_preview (2015-08-24 to 2015-08-31) v322

• src/hg/cirm/cdw/flowCharts/sqlToTxt/makefile
  • lines changed 4, context: html, text, full: html, text
    Makefile for sqlToTxt.c
    
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 3, context: html, text, full: html, text
    Add comment as per code review. (no redmine)
    
• src/hg/htdocs/images/phylo/hg38_100way.png
  • lines changed 0, context: html, text, full: html, text
    common name tree for hg38 100-way refs #14560
    
  • lines changed 0, context: html, text, full: html, text
    fixing broken names refs #14560
    
  • lines changed 0, context: html, text, full: html, text
    update brush tailed rat name refs #14560
    
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    removing link to davis bioinformatics as they did not add the workshop there yet. adding link to host page higher up on the page
    
• src/hg/htdocs/training/trainingMap.html
  • lines changed 4, context: html, text, full: html, text
    adding commented-out parameters for maps so mirrors can have custom centering. one each for euronode and soon-to-be asianode
    
• src/hg/js/model/lib/cart.js
  • lines changed 1, context: html, text, full: html, text
    Changing a call to $.isPlainObject to _.isPlainObject for consistency (thanks Max). refs #15912
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    Fixing logical mixup between 'est' and 'all_est' -- symptom was checkTableCoords making a bad sql query, found by Hiram.
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 25, context: html, text, full: html, text
    procedure for SGP Gene track refs #13214
    
• src/hg/makeDb/doc/ce11/multiz26way.txt
  • lines changed 103, context: html, text, full: html, text
    ready for phastCons phyloP runs refs #15209
    
• src/hg/makeDb/doc/genomeCoverage.txt
  • lines changed 203, context: html, text, full: html, text
    capturing data about correspondence between UCSC database and external resources refs #15209
    
• src/hg/makeDb/doc/genomeInformationSites.txt
  • lines changed 129, context: html, text, full: html, text
    capturing data about correspondence between UCSC database and external resources refs #15209
    
• src/hg/makeDb/doc/genomeSourceSites.txt
  • lines changed 149, context: html, text, full: html, text
    capturing data about correspondence between UCSC database and external resources refs #15209
    
• src/hg/makeDb/doc/hg38/hg19MassiveLift.txt
  • lines changed 9, context: html, text, full: html, text
    Added the hgIkmcExtra table documentation, refs # 15518
    
• src/hg/makeDb/doc/hg38/stsMap.txt
  • lines changed 1, context: html, text, full: html, text
    status to DONE from WORKING refs #15524
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ci3 - Ciona intestinalis refs #15796
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    Added ci3 Ciona intestnalis; refs #15796
    
  • lines changed 17, context: html, text, full: html, text
    Added ancCey1 - A. ceylanicum refs #15209
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    Added ci3 - Ciona intestinalis refs #15796
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added ancCeyNames - A. ceylanicum refs #15209
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 25, context: html, text, full: html, text
    adding ci3 and fixing all the ensGene tracks refs #15796
    
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/cow/bosTau8/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    adding search rules for these new tables refs #13214
    
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    adding search rules for these new tables refs #13214
    
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 3, context: html, text, full: html, text
    changed the html pages to keep up with changing ABT to ABTutu so the archibishop is more obvious, per code review. refs #15909
    
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • lines changed 3, context: html, text, full: html, text
    changed the html pages to keep up with changing ABT to ABTutu so the archibishop is more obvious, per code review. refs #15909
    
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 3, context: html, text, full: html, text
    changed the html pages to keep up with changing ABT to ABTutu so the archibishop is more obvious, per code review. refs #15909
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding an overide for the coriell del dup track, refs #15534
    
  • lines changed 11, context: html, text, full: html, text
    adding search rules for these new tables refs #13214
    
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 8, context: html, text, full: html, text
    Updating link outs and track description page links for IKMC track on human, refs #15518
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Turning off exon numbering for IKMC track on human as it doesn't make sense, refs #15518
    
  • lines changed 2, context: html, text, full: html, text
    Updating link outs and track description page links for IKMC track on human, refs #15518
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    adding search rules for these new tables refs #13214
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    adding search rules for these new tables refs #13214
    
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    updated with geneid search rules refs #13214
    
• src/hg/makeDb/trackDb/trackDb.chainNet.nematode.ra
  • lines changed 55, context: html, text, full: html, text
    eliminate stray release alpha tags causing trouble with tdbQuery release checks refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/burXyl1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeAng2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeJap4/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeJap4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caePb3/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caePb3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeRem4/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeRem4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp111/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp111/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/caeSp51/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/cb4/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/cb4/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/dirImm1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/haeCon2/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/haeCon2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/melHap1/trackDb.chainNet.ra
  • lines changed 159, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/melHap1/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/melInc2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/panRed1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/priPac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/strRat2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
  • lines changed 40, context: html, text, full: html, text
    eliminate stray release alpha tags causing trouble with tdbQuery release checks refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/triSpi1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/makeDb/trackDb/worm/triSui1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chainNet priorities refs #15209
    
• src/hg/phyloGif/phyloGif.c
  • lines changed 72, context: html, text, full: html, text
    fix phyloGif to accept more special chars. fixes #15919
    
• src/hg/utils/phyloTrees/ce11.26way.commonNames.nh
  • lines changed 26, context: html, text, full: html, text
    after phyloFit from 26-way alignment refs #15209
    
• src/hg/utils/phyloTrees/ce11.26way.dissect.txt
  • lines changed 357, context: html, text, full: html, text
    for calculating chainNet override priorities refs #15209
    
• src/hg/utils/phyloTrees/ce11.26way.nh
  • lines changed 26, context: html, text, full: html, text
    after phyloFit from 26-way alignment refs #15209
    
• src/hg/utils/phyloTrees/ce11.26way.scientificNames.nh
  • lines changed 26, context: html, text, full: html, text
    after phyloFit from 26-way alignment refs #15209
    
• src/hg/utils/phyloTrees/ce11.commonNames.nh
  • lines changed 26, context: html, text, full: html, text
    after phyloFit from 26-way alignment refs #15209
    
  • lines changed 26, context: html, text, full: html, text
    finish removal of ce11.commonNames.sh
    
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 34, context: html, text, full: html, text
    adding the nematodes and some name corrections refs #15209
    
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 4, context: html, text, full: html, text
    adding catAur1 chaPel1 nesNot1 podCri1 refs #14560
    
• src/hg/utils/phyloTrees/worms26way.chainNet.pl
  • lines changed 196, context: html, text, full: html, text
    for calculating chainNet override priorities refs #15209
    
• src/lib/phyloTree.c
  • lines changed 77, context: html, text, full: html, text
    fix phyloGif to accept more special chars. fixes #15919
    
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    fixup the utils-alpha target so it will make binaries in src/utils/ refs #15836
    
• src/utils/bigWigMerge/bigWigMerge.c
  • lines changed 12, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/makefile
  • lines changed 9, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/test/expected/12merge.bedGraph
  • lines changed 4, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/test/expected/21merge.bedGraph
  • lines changed 3, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/test/in/hg19.chrom.sizes
  • lines changed 93, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/test/in/t1.bed
  • lines changed 2, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/test/in/t2.bed
  • lines changed 1, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/expected/12merge.bedGraph
  • lines changed 4, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/expected/12merge.max.bedGraph
  • lines changed 2, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/expected/21merge.bedGraph
  • lines changed 4, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/expected/21merge.max.bedGraph
  • lines changed 2, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/in/hg19.chrom.sizes
  • lines changed 93, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/in/t1.bed
  • lines changed 2, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/in/t2.bed
  • lines changed 1, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
• src/utils/bigWigMerge/tests/makefile
  • lines changed 25, context: html, text, full: html, text
    add -max option to bigWigMerge #15929
    
  • lines changed 5, context: html, text, full: html, text
    Added clean target so 'make clean' in kent/src doesn't break. Removed unused tmp dir.
    
  • lines changed 1, context: html, text, full: html, text
    fiddle with bigWigMerge/tests/makefile
    
  • lines changed 6, context: html, text, full: html, text
    Mend:wqrge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v322 preview1 refs #15836
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    adding .soe.ucsc.edu to victim code summary message email To: field refs #15836
    

• lines changed: 6074
• files changed: 131