All File Changes

v325_preview2 to v325_base (2015-11-09 to 2015-11-16) v325

• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 47, context: html, text, full: html, text
    adding descriptions to dataset overview page, refs #16300
    
• src/hg/cirm/cdw/inc/cdwDataset.h
  • lines changed 67, context: html, text, full: html, text
    adding descriptions to dataset overview page, refs #16300
    
• src/hg/cirm/cdw/lib/cdwDataset.as
  • lines changed 9, context: html, text, full: html, text
    adding descriptions to dataset overview page, refs #16300
    
• src/hg/cirm/cdw/lib/cdwDataset.c
  • lines changed 150, context: html, text, full: html, text
    adding descriptions to dataset overview page, refs #16300
    
• src/hg/cirm/cdw/lib/cdwDataset.sql
  • lines changed 15, context: html, text, full: html, text
    adding descriptions to dataset overview page, refs #16300
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 8, context: html, text, full: html, text
    fix problem that Galt found with leaking sql connections (no redmine)
    
• src/hg/hgTracks/extTools.ra
  • lines changed 31, context: html, text, full: html, text
    adding crispor back to external tools and sending them info they need to
    build custom tracks, refs #16308
    
  • lines changed 2, context: html, text, full: html, text
    moving onlyDbs into the right stanza, refs #16308
    
• src/hg/hgc/hgc.c
  • lines changed 11, context: html, text, full: html, text
    more work on bigChain
    
• src/hg/inc/chainNetDbLoad.h
  • lines changed 7, context: html, text, full: html, text
    more work on bigChain
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v325
    
• src/hg/js/react/lib/PositionSearch.jsx
  • lines changed 27, context: html, text, full: html, text
    The position/search autocomplete was initialized once when the input component
    was mounted -- which caused incorrect behavior if one then changed to a different
    db. Now it is initialized once regardless of whether the initial db has a gene
    suggest track, but always uses the current db and gene track if applicable.
    fixes #16371
    
• src/hg/lib/chainNetDbLoad.c
  • lines changed 74, context: html, text, full: html, text
    more work on bigChain
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 9, context: html, text, full: html, text
    Adding the new html file for tRNA tracks and documentation. refs #15107
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 12, context: html, text, full: html, text
    Adding the new html file for tRNA tracks and documentation. refs #15107
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 66, context: html, text, full: html, text
    Fix URLs in cv.ra and wgEncodeCell table. refs #16364
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    fixed warning in gencode load makefile
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Lower minCheck for some GENCODE VM7 Tables per Marks request, refs #16129
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 16, context: html, text, full: html, text
    Updating blastz to lastz on conservation track description page, refs #16321
    
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 10, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 21, context: html, text, full: html, text
    Fix URLs in cv.ra and wgEncodeCell table. refs #16364
    
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 2, context: html, text, full: html, text
    Fixed typo on description page, refs #15616
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling error in Yale Pseudogenes table
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3.html
  • lines changed 47, context: html, text, full: html, text
    Updating references and some formatting for 1000 Genomes Ph 3 track desc pages, refs #14325
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3Accessibility.html
  • lines changed 53, context: html, text, full: html, text
    Updating references and some formatting for 1000 Genomes Ph 3 track desc pages, refs #14325
    
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.ra
  • lines changed 2, context: html, text, full: html, text
    Turning off VM4 by default, refs #16129
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.html
  • lines changed 9, context: html, text, full: html, text
    Changes to contributor list, refs #16129
    
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 10, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • lines changed 18, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 18, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 10, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/tRNAs.html
  • lines changed 7, context: html, text, full: html, text
    Adding the new html file for tRNA tracks and documentation. refs #15107
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 1, context: html, text, full: html, text
    Updating Conservation track page to show switch from blastz to lastz
    
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding a release alpha tag for the tRNAs track update. refs #15107
    
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 17, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 16, context: html, text, full: html, text
    Updating Conservation Description Pages to reference lastz instead of blastz, for all orgs updated after 2009, refs #16321
    
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 6, context: html, text, full: html, text
    clinvar changed their format again. Also fixing "more than 10" to
    something more readable. refs #16292
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v325 final build refs #16299
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    fixup build meister email specification refs #16299
    
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/doLiftOverTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 2, context: html, text, full: html, text
    BUILDMEISTER is already a fully qualified address refs #16299
    
  • lines changed 2, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
  • lines changed 2, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • lines changed 1, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    
• src/utils/qa/weeklybld/moveBranchTag.csh
  • lines changed 1, context: html, text, full: html, text
    fixup build meister email specification refs #16299doHgNearTestRobot.csh
    

• lines changed: 1144
• files changed: 67