All File Changes

v280_preview to v280_preview2 (2013-02-19 to 2013-02-26) v280

• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    don't check for assembly database on close of sql connection (per code review 10237)
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    don't check for assembly database on close of sql connection (per code review 10237)
• src/hg/hgTables/joining.c
  • lines changed 2, context: html, text, full: html, text
    don't check for assembly database on close of sql connection (per code review 10237)
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    cosmic is changing its WEB site URL redmine 9386
  • lines changed 1, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/htdocs/goldenPath/help/cutters.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links as per redmine #10218.
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 3, context: html, text, full: html, text
    Fixed broken links as per redmine #10218.
• src/hg/inc/trackHub.h
  • lines changed 2, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
  • lines changed 19, context: html, text, full: html, text
    clean up comments to start with a capital and end with a period (per code review #10237)
  • lines changed 1, context: html, text, full: html, text
    free list of chrom names from twoBit library, change trackHubGetHubLabels to trackHubGetCladeLables (from code review #10237)
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    Add db and hgsid to getDna link activated by right-click on an hgTracks item. Bug #10276
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/lib/cytoBandIdeo.sql
  • lines changed 5, context: html, text, full: html, text
    added some chars to index to accommodate larger chromNames. changed description of some fields
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    add comment to somewhat funky mapping of the field "genome" to the field "organism" when using track hubs since track hubs call the assembly name "genome" per code review #10237
  • lines changed 19, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
  • lines changed 27, context: html, text, full: html, text
    clean up comments to start with a capital and end with a period (per code review #10237)
  • lines changed 10, context: html, text, full: html, text
    free list of chrom names from twoBit library, change trackHubGetHubLabels to trackHubGetCladeLables (from code review #10237)
  • lines changed 4, context: html, text, full: html, text
    oops, misspelled slFreeList as slListFree (from code review #10237)
  • lines changed 4, context: html, text, full: html, text
    I added an errAbort for the two cases that assume the hash is initialized (trackHubAssemblyField and trackHubDbDbFromAssemblyDb) (from code review #10237)
  • lines changed 11, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    change trackHubRemoveHubName to trackHubSkipName (per code review #10237)
  • lines changed 1, context: html, text, full: html, text
    free list of chrom names from twoBit library, change trackHubGetHubLabels to trackHubGetCladeLables (from code review #10237)
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic track to v63
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1436, context: html, text, full: html, text
    redmine #9407n ensemble gene v70 update done.
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 545, context: html, text, full: html, text
    Adding makedoc for new assembly redmine #9812
  • lines changed 15, context: html, text, full: html, text
    Completing first section of new assembly browser building.
• src/hg/makeDb/doc/oreNil1.txt
  • lines changed 10, context: html, text, full: html, text
    add assembly information from NCBI
• src/hg/makeDb/doc/rn5.txt
  • lines changed 9, context: html, text, full: html, text
    monDom5 rn5 chaining is failing
• src/hg/makeDb/hgLoadOut/makefile
  • lines changed 3, context: html, text, full: html, text
    adding compile rule for debugging in this directory
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Changed hgnc to hgncXref (redmine #10268)
  • lines changed 1, context: html, text, full: html, text
    Changed knownXref section to be human-specific (redmine #10268)
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Copying alpha cv.ra to beta and public
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Copying alpha cv.ra to beta and public
• src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html
  • lines changed 63, context: html, text, full: html, text
    Adding nomLeu3 files.
• src/hg/makeDb/trackDb/gibbon/nomLeu3/gap.html
  • lines changed 33, context: html, text, full: html, text
    Adding nomLeu3 files.
• src/hg/makeDb/trackDb/gibbon/nomLeu3/gold.html
  • lines changed 33, context: html, text, full: html, text
    Adding nomLeu3 files.
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Adding nomLeu3 files.
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 5, context: html, text, full: html, text
    Editing sentence and pubmed references for dgv.html, code review with Steve #10235
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.ra
  • lines changed 1, context: html, text, full: html, text
    Adjusting default signal view setting for UW Histone track, Release 5 on RR, lab request of change from 1:10 to 1:100, Cricket forwarded email from Richard Sandstrom
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cosmic is changing its WEB site URL redmine 9386
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    added felCat5 to list of genome
  • lines changed 1, context: html, text, full: html, text
    Adding nomLeu3 to makefile.
• src/hg/makeDb/trackDb/mouse/cytoBand.html
  • lines changed 7, context: html, text, full: html, text
    changed longLabel and description page to something more generic. user complained that text was human-centric (RM #9994)
  • lines changed 1, context: html, text, full: html, text
    dropped a BR tag not needed
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1Composite.ra
  • lines changed 93, context: html, text, full: html, text
    removed obsolete mm10Strains1Composite.ra
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    changed longLabel and description page to something more generic. user complained that text was human-centric (RM #9994)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    added cytoBandIdeo at top level for new navigation on orgs with no cytology
  • lines changed 2, context: html, text, full: html, text
    turned off publication gene & band subtracks, per redmine #6833
  • lines changed 2, context: html, text, full: html, text
    undoing last change
• src/hg/makeDb/trackDb/ucscGenePfam.html
  • lines changed 3, context: html, text, full: html, text
    Added a link to the download page for pslMap (redmine #9135)
• src/hg/utils/automation/ensGene/melGal1.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    redmine #9407 need to lift ensemble's MT to ucsc's chrM for melGal1
• src/hg/utils/automation/ensGene/mm10.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    Feedback from Hiram, use sed delete commands on the name translation rule to remove PATCH name form mm10.
• src/inc/common.h
  • lines changed 2, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/inc/twoBit.h
  • lines changed 2, context: html, text, full: html, text
    add a comment to twoBitOpenExt (#8072)
  • lines changed 6, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/lib/common.c
  • lines changed 6, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/lib/twoBit.c
  • lines changed 44, context: html, text, full: html, text
    modify twoBit library to auto-recognize whether it's dealing with a URL or local file (per code review #10237)
• src/utils/faToTwoBit/faToTwoBit.c
  • lines changed 2, context: html, text, full: html, text
    add clean makefile target and expand description of ignoreDups usage message
• src/utils/faToTwoBit/makefile
  • lines changed 4, context: html, text, full: html, text
    add clean makefile target and expand description of ignoreDups usage message
• src/utils/qa/makeCytoBandIdeo.csh
  • lines changed 101, context: html, text, full: html, text
    script to make an ideogram for orgs with no cytology
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    script to make an ideogram for orgs with no cytology
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v280 preview2

• lines changed: 2647
• files changed: 69