All File Changes

v311_base to v312_preview (2015-01-26 to 2015-02-02) v312

• src/browserbox/makefile
  • lines changed 6, context: html, text, full: html, text
    adding possibility to force auto updates to off in gbib, refs #14602
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 26, context: html, text, full: html, text
    adding possibility to force auto updates to off in gbib, refs #14602
    
• src/hg/hgAi/hgAi.c
  • lines changed 6, context: html, text, full: html, text
    Add yet another special case for all_* tables.
    
• src/hg/hgTables/schema.c
  • lines changed 2, context: html, text, full: html, text
    Fixed a bug that caused split tables to crash in the browser
    
• src/hg/hgTracks/config.c
  • lines changed 6, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
• src/hg/hgTracks/retroGene.c
  • lines changed 9, context: html, text, full: html, text
    update hard-coded list of retrogene tracks to register
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 227, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
• src/hg/hgc/retroClick.c
  • lines changed 1, context: html, text, full: html, text
    Removed description line which would only appear on the details page and merged it with the existing Description section in the HTML description page.
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 3, context: html, text, full: html, text
    Adding link in GBiB help doc to Assembly Hub step-by-step example
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 39, context: html, text, full: html, text
    Adding notes to Track Hub User Guide about new Assembly QuickStart Guide, and updating Hub Connection process
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 259, context: html, text, full: html, text
    Adding quick start guide to assembly hubs with blat documentation
    
  • lines changed 28, context: html, text, full: html, text
    Adding notes to Track Hub User Guide about new Assembly QuickStart Guide, and updating Hub Connection process
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    Documents new trackDb setting exonNumbers 7474
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 3, context: html, text, full: html, text
    Documents new trackDb setting exonNumbers 7474
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 12, context: html, text, full: html, text
    Documents new trackDb setting exonNumbers 7474
    
  • lines changed 1, context: html, text, full: html, text
    adding type psl to list of allowed types for new exonNumbers setting
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    Staging entries for relaunch of training intake survey. refs #14714
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 6, context: html, text, full: html, text
    Adding Ebola paper to pubs.
    
  • lines changed 14, context: html, text, full: html, text
    first pub of 2015
    
• src/hg/htdocs/images/training/vidTitle06.jpg
  • lines changed 0, context: html, text, full: html, text
    adding title slides for vids 06, 07. refs #13969
    
• src/hg/htdocs/images/training/vidTitle07.jpg
  • lines changed 0, context: html, text, full: html, text
    adding title slides for vids 06, 07. refs #13969
    
• src/hg/htdocs/indexNews.html
  • lines changed 35, context: html, text, full: html, text
    Abridged entries were missing for last 3 announcements. Prepping for survey relaunch. refs #14714
    
  • lines changed 22, context: html, text, full: html, text
    Staging entries for relaunch of training intake survey. refs #14714
    
• src/hg/js/hgTracks.js
  • lines changed 17, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
• src/hg/js/react/hgAi/hgAi.jsx
  • lines changed 32, context: html, text, full: html, text
    Minor refactoring: instead of passing a schema link object into AddDataSource,
    make it locally.
    
• src/hg/lib/cartJson.c
  • lines changed 14, context: html, text, full: html, text
    All Tracks / All Tables groups are not yet working in hgAi; I have a
    plan to fix it right, but for now, just omit those groups.
    refs #14579
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 79, context: html, text, full: html, text
    lastz chain net liftOver files for user request refs #14625
    
• src/hg/makeDb/doc/danRer10/initialBuild.txt
  • lines changed 105, context: html, text, full: html, text
    now running genbank refs #14017
    
  • lines changed 19, context: html, text, full: html, text
    liftOver to danRer7 refs #14017
    
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 15, context: html, text, full: html, text
    liftOver to danRer10 refs #14017
    
• src/hg/makeDb/doc/eboVir3/gbkToGp.pl
  • lines changed 1, context: html, text, full: html, text
    update 2015-01-06 refs #14278
    
• src/hg/makeDb/doc/eboVir3/newSequences.txt
  • lines changed 49, context: html, text, full: html, text
    update 2015-01-06 refs #14278
    
  • lines changed 6, context: html, text, full: html, text
    update added KP658432v1 KP342330v1 refs #14278
    
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 79, context: html, text, full: html, text
    lastz chain net liftOver files for user request refs #14625
    
• src/hg/makeDb/doc/felCat8/initialBuild.txt
  • lines changed 8, context: html, text, full: html, text
    felCat8 in the pushQ refs #14412
    
• src/hg/makeDb/doc/felCat8/lastzRuns.txt
  • lines changed 73, context: html, text, full: html, text
    felCat8 in the pushQ refs #14412
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 18, context: html, text, full: html, text
    Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
    than twice the number of rows in the snp table with that exception.
    Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
    counts. Note: ExceptionDesc counts can still be slightly higher than
    snp table counts because several exceptions are logged before the point
    at which we decide whether to keep or discard a variant.
    refs #14189
    
  • lines changed 0, context: html, text, full: html, text
    lastz chain net liftOver files for user request refs #14625
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 11, context: html, text, full: html, text
    Add tool to check links in a table (based on columnName 'url')
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 18, context: html, text, full: html, text
    Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
    than twice the number of rows in the snp table with that exception.
    Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
    counts. Note: ExceptionDesc counts can still be slightly higher than
    snp table counts because several exceptions are logged before the point
    at which we decide whether to keep or discard a variant.
    refs #14189
    
• src/hg/makeDb/doc/macFas5/initialBuild.txt
  • lines changed 20, context: html, text, full: html, text
    in the pushQ refs #11174
    
• src/hg/makeDb/doc/macFas5/lastzRuns.txt
  • lines changed 151, context: html, text, full: html, text
    in the pushQ refs #11174
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 0, context: html, text, full: html, text
    lastz chain net liftOver files for user request refs #14625
    
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 49, context: html, text, full: html, text
    lastz chain net liftOver files for user request refs #14625
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added danRer10 - Zebrafish refs #14017
    
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    some moving around of data on the euronode
    
• src/hg/makeDb/genbank/etc/euronode-dbload
  • lines changed 2, context: html, text, full: html, text
    some moving around of data on the euronode
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    Added danRer10; refs #14017
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added danRer10 - Zebrafish refs #14017
    
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 13, context: html, text, full: html, text
    new things for the genbank pipeline to ignore
    
  • lines changed 1, context: html, text, full: html, text
    another thing for genbank to ignore
    
  • lines changed 1, context: html, text, full: html, text
    another thing to ignore from genbank
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    Removing merge conflict caught by Kate. refs #14740
    
  • lines changed 11, context: html, text, full: html, text
    adding danRer10 rules refs #14017
    
• src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
  • lines changed 2, context: html, text, full: html, text
    adding KP342330.1 KP658432.1 refs #14278
    
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 1, context: html, text, full: html, text
    adding KP342330.1 KP658432.1 refs #14278
    
  • lines changed 1, context: html, text, full: html, text
    correct ordering KP342330.1 KP658432.1 refs #14278
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 65, context: html, text, full: html, text
    Clean up hg19 ENCODE Regulation track defaults on genome-test
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed the nextItemButton setting for Retroposed Genes V9.
    
  • lines changed 2, context: html, text, full: html, text
    Changing shortLabel and turning off mouseover exon numbering for Retroposed genes track on mm10,hg38. refs #14719 #14720
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added wgEncodeReg.ra to the file
    
• src/hg/makeDb/trackDb/human/hg38/ucscRetroAli9.html
  • lines changed 6, context: html, text, full: html, text
    Merged a track description hard-coded in retroClick.c (hgc) into the Description section in the HTML description page.
    
• src/hg/makeDb/trackDb/human/hg38/uwDnase.ra
  • lines changed 421, context: html, text, full: html, text
    Polish track labels. Change defaults to be cell types in ENCODE Reg Txn track. refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 384, context: html, text, full: html, text
    Created a .ra file describing the ENCODE Regulatory basic tracks
    
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 16, context: html, text, full: html, text
    Correcting the names of the dbSNP download files since they now tweak the paths for human.
    refs #14189
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed the nextItemButton setting for Retroposed Genes V6.
    
  • lines changed 2, context: html, text, full: html, text
    Changing shortLabel and turning off mouseover exon numbering for Retroposed genes track on mm10,hg38. refs #14719 #14720
    
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli6.html
  • lines changed 6, context: html, text, full: html, text
    Merged a track description hard-coded in retroClick.c (hgc) into the Description section in the HTML description page.
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Fixes #7474 - mouseover now shows exon and intron numbers for linkedFeatures tracks.
    
  • lines changed 1, context: html, text, full: html, text
    adding type psl to list of allowed types for new exonNumbers setting
    
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 4, context: html, text, full: html, text
    Jonathan found that snp*ExceptionDesc's NonIntegerChromCount was more
    than twice the number of rows in the snp table with that exception.
    Turns out it was incremented in a loop on alleles. Rebuilt w/corrected
    counts. Note: ExceptionDesc counts can still be slightly higher than
    snp table counts because several exceptions are logged before the point
    at which we decide whether to keep or discard a variant.
    refs #14189
    
• src/hg/utils/checkUrlsInTable/checkUrlsInTable.c
  • lines changed 76, context: html, text, full: html, text
    Tool for checking metadata term tables (and any others having a column with urls
    
• src/hg/utils/checkUrlsInTable/makefile
  • lines changed 4, context: html, text, full: html, text
    Makefile for table checker
    
• src/hg/utils/makefile
  • lines changed 13, context: html, text, full: html, text
    Add tool to check links in a table (based on columnName 'url')
    
  • lines changed 1, context: html, text, full: html, text
    fixed plurality typo - script is checkUrlsInTable, not Tables
    
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    don't flush stdin magic handle on close
    
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    incremented bedToBigBed version to 2.7
    
  • lines changed 1, context: html, text, full: html, text
    explained comment better
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v312 preview1 refs #14768
    

• lines changed: 2564
• files changed: 81