All File Changes

v366_base to v367_preview (2018-05-29 to 2018-06-04) v367

• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    99ddcee8146ff079470bf466ca5013c97afcd72a Fri Jun 1 17:23:42 2018 -0700
    Fixing downloads against old filter method replaced by faceted search. fixes #21511
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 2, context: html, text, full: html, text
    d5dc819dcd53f75ec8afa1ab4929dee83ceb171a Sat Jun 2 09:45:35 2018 -0700
    genome-centdb.hgcentral.userDb has finally exceeded the old limit which was 14 GB. I have increased it to 20 GB. hgcentral SSD on hgnfs1 is only 14% full, so it has plenty of space left. It seems the table has been slowly growing, not some sudden rapid increase.
  • lines changed 1, context: html, text, full: html, text
    3bbfabb0927ac2ae9a976a018145b3314cc2e86e Sun Jun 3 12:06:34 2018 -0700
    fixing email address by adding a proper domain.
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 10, context: html, text, full: html, text
    2fcac36b4315e9fdafc5b96a43a5898f99d66e62 Tue May 29 10:32:20 2018 -0700
    adding blat 32 limit to faq, refs #21523
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    906f2f040a6fd2277cffe12d1826f1d589484562 Wed May 30 14:30:10 2018 -0700
    address Safari problem where the ready function isn't called after back button. (#21540)
• src/hg/lib/lrg.c
  • lines changed 48, context: html, text, full: html, text
    81b2ee7407e5916847893c4851b38e0788efe728 Wed May 30 15:07:16 2018 -0700
    LRG mappings to the reference genomes used to always span the entire LRG, but they don't anymore; there may be one mapping that spans the entire LRG and another mapping that spans only part of it. Instead of assuming that lrgStart is 0 and lrgEnd is size, detect if they're not, and in that case bundle lrgStart and lrgEnd into the name field and parse back out when making PSL. sorta refs #13359 #17877
• src/hg/makeDb/doc/hg19.txt
  • lines changed 24, context: html, text, full: html, text
    b55093589f69c02a2bd605a3334758d02aecc011 Wed May 30 17:44:47 2018 -0700
    Update LRG process to support alt haplotypes and patches. refs #18853
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 16, context: html, text, full: html, text
    b55093589f69c02a2bd605a3334758d02aecc011 Wed May 30 17:44:47 2018 -0700
    Update LRG process to support alt haplotypes and patches. refs #18853
• src/hg/makeDb/doc/hg38/miRnaAtlas.txt
  • lines changed 95, context: html, text, full: html, text
    0eedd7a9395ff7e38bf9a7c84fe2c569f00a5ed3 Fri Jun 1 11:42:45 2018 -0700
    miRna tissue atlas barChart track in progress, refs #18508
• src/hg/makeDb/doc/hg38/wgRna.txt
  • lines changed 52, context: html, text, full: html, text
    7eceec4d18f6c7acb2f7a10c4ad78d15c3b7362f Wed May 30 14:00:27 2018 -0700
    makedoc for miRNA track update, refs #21516
  • lines changed 3, context: html, text, full: html, text
    959343a37a03a64e63f95c1386a4ebc63b59fcbc Wed May 30 15:42:03 2018 -0700
    Adding note about color-coding to new non-coding rna tracks, refs #21516
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    781f82198d84bc53e75ec703e3a6fa6d9fcd878f Fri Jun 1 08:32:29 2018 -0700
    Removing pennantIcons per cronjob, removing GENCODE hg19/hg38 new markings
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV28lift37.ra
  • lines changed 1, context: html, text, full: html, text
    781f82198d84bc53e75ec703e3a6fa6d9fcd878f Fri Jun 1 08:32:29 2018 -0700
    Removing pennantIcons per cronjob, removing GENCODE hg19/hg38 new markings
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    781f82198d84bc53e75ec703e3a6fa6d9fcd878f Fri Jun 1 08:32:29 2018 -0700
    Removing pennantIcons per cronjob, removing GENCODE hg19/hg38 new markings
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    0eedd7a9395ff7e38bf9a7c84fe2c569f00a5ed3 Fri Jun 1 11:42:45 2018 -0700
    miRna tissue atlas barChart track in progress, refs #18508
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV28.ra
  • lines changed 1, context: html, text, full: html, text
    781f82198d84bc53e75ec703e3a6fa6d9fcd878f Fri Jun 1 08:32:29 2018 -0700
    Removing pennantIcons per cronjob, removing GENCODE hg19/hg38 new markings
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 8, context: html, text, full: html, text
    e7a1b6c30141800a507072182d4e7105121ba878 Tue May 29 13:10:08 2018 -0700
    Updating redirected links for petMar2, uiLinks cronjob.
• src/hg/makeDb/trackDb/lamprey/petMar2/lampreyGene.html
  • lines changed 1, context: html, text, full: html, text
    e7a1b6c30141800a507072182d4e7105121ba878 Tue May 29 13:10:08 2018 -0700
    Updating redirected links for petMar2, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    edfce0ad33dda94aa1dfd02a2d98656155b083c5 Tue May 29 13:08:11 2018 -0700
    Adding the 'update' pennantIcon for the new UCSC Genes (v17) for mm10, refs #19786
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 8, context: html, text, full: html, text
    9110bc70401002d5d57360d337e3a5653179cbc7 Thu May 31 09:04:38 2018 -0700
    Updating redirected links for rn5, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
  • lines changed 2, context: html, text, full: html, text
    a5343b2938dbb4a9264e39ebbd9245720bbcb564 Mon Jun 4 08:08:30 2018 -0700
    Updating redirected links for cb1, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
  • lines changed 2, context: html, text, full: html, text
    a5343b2938dbb4a9264e39ebbd9245720bbcb564 Mon Jun 4 08:08:30 2018 -0700
    Updating redirected links for cb1, uiLinks cronjob.
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 12, context: html, text, full: html, text
    81b2ee7407e5916847893c4851b38e0788efe728 Wed May 30 15:07:16 2018 -0700
    LRG mappings to the reference genomes used to always span the entire LRG, but they don't anymore; there may be one mapping that spans the entire LRG and another mapping that spans only part of it. Instead of assuming that lrgStart is 0 and lrgEnd is size, detect if they're not, and in that case bundle lrgStart and lrgEnd into the name field and parse back out when making PSL. sorta refs #13359 #17877
  • lines changed 42, context: html, text, full: html, text
    b55093589f69c02a2bd605a3334758d02aecc011 Wed May 30 17:44:47 2018 -0700
    Update LRG process to support alt haplotypes and patches. refs #18853
• src/utils/bedJoinTabOffset
  • lines changed 1, context: html, text, full: html, text
    87a97a7184d29e9008cc1049501b33869ee751bb Fri Jun 1 08:58:49 2018 -0700
    fixing KeyError in bedJoinTabOffset when there are multiple bed keys that map to one tabFile to join to, refs #18508
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    cad7006bb9c8e7cb011882ed02639218dccfd5e0 Mon Jun 4 09:09:39 2018 -0700
    v367 preview1

• lines changed: 354
• files changed: 26