All File Changes

v340_preview2 to v340_base (2016-10-10 to 2016-10-17) v340

• src/README
  • lines changed 4, context: html, text, full: html, text
    a3ef3c95bc7b21a5c2867c18261215929f3c651e Wed Oct 5 14:40:50 2016 -0700
    Adding bits about global naming convention.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.c
  • lines changed 92, context: html, text, full: html, text
    3bb0ec131c2593c99227ab2adca7aa59a30ce7d6 Wed Oct 12 13:30:53 2016 -0700
    Adding in auxilary cdwWebBrowse files, refs #18780
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.h
  • lines changed 1, context: html, text, full: html, text
    3bb0ec131c2593c99227ab2adca7aa59a30ce7d6 Wed Oct 12 13:30:53 2016 -0700
    Adding in auxilary cdwWebBrowse files, refs #18780
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.h
  • lines changed 8, context: html, text, full: html, text
    3bb0ec131c2593c99227ab2adca7aa59a30ce7d6 Wed Oct 12 13:30:53 2016 -0700
    Adding in auxilary cdwWebBrowse files, refs #18780
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
  • lines changed 8, context: html, text, full: html, text
    3bb0ec131c2593c99227ab2adca7aa59a30ce7d6 Wed Oct 12 13:30:53 2016 -0700
    Adding in auxilary cdwWebBrowse files, refs #18780
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 85, context: html, text, full: html, text
    2aed0ce4fada5b1e2ea7fcb96d795c0544db0ec5 Wed Oct 12 13:20:30 2016 -0700
    Adding in the new search bar and fixing up the dataset page permissions, refs #17870
    
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 2, context: html, text, full: html, text
    3bb0ec131c2593c99227ab2adca7aa59a30ce7d6 Wed Oct 12 13:30:53 2016 -0700
    Adding in auxilary cdwWebBrowse files, refs #18780
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 71, context: html, text, full: html, text
    d9db54ea71dbefb96669c515745b5174c8565a03 Wed Oct 12 10:09:37 2016 -0700
    Updating autosql generated files to correspond with cdw.as
    
  • lines changed 71, context: html, text, full: html, text
    f5cfe6f7788816ba63c0f15ae3574ed9468a6640 Wed Oct 12 13:26:28 2016 -0700
    adding in the jointDataset table
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 178, context: html, text, full: html, text
    d9db54ea71dbefb96669c515745b5174c8565a03 Wed Oct 12 10:09:37 2016 -0700
    Updating autosql generated files to correspond with cdw.as
    
  • lines changed 178, context: html, text, full: html, text
    f5cfe6f7788816ba63c0f15ae3574ed9468a6640 Wed Oct 12 13:26:28 2016 -0700
    adding in the jointDataset table
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 13, context: html, text, full: html, text
    d9db54ea71dbefb96669c515745b5174c8565a03 Wed Oct 12 10:09:37 2016 -0700
    Updating autosql generated files to correspond with cdw.as
    
  • lines changed 13, context: html, text, full: html, text
    c7989aaf9a5d9f9f77eed8f04bf904f1da0b931b Wed Oct 12 13:25:05 2016 -0700
    adding in the jointDataset table
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    2ff236a2b0d3a7382bbfae2816dc410c4f8e96b8 Mon Oct 10 16:45:07 2016 -0700
    This seems to be unnecessary at this time and may mess up cartJson.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    e9644c89c5b4efb353847f47a16b90df3af9c12c Mon Oct 10 15:15:24 2016 -0700
    pay attention to super track URL settings when hideTracks=1 is set.
    
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    7e6fe97d6d581f789137df6a01edb603954608c2 Fri Oct 14 10:18:19 2016 -0700
    hgVai's UI default for whether to match up input variants with dbSNP is true but the execution part's default was false -- making it consistent with UI default.
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 20, context: html, text, full: html, text
    05bace9a237244f04fd73e2f7fbb7a6de5f09fe8 Mon Oct 17 09:52:04 2016 -0700
    added news announcement for HGVS format, refs #15071
    
• src/hg/htdocs/indexNews.html
  • lines changed 7, context: html, text, full: html, text
    05bace9a237244f04fd73e2f7fbb7a6de5f09fe8 Mon Oct 17 09:52:04 2016 -0700
    added news announcement for HGVS format, refs #15071
    
  • lines changed 4, context: html, text, full: html, text
    4f00c10f8fecf4123f5f6011006be9b7013deb97 Mon Oct 17 09:54:35 2016 -0700
    pasted wrong entry, fixing
    
• src/hg/inc/mdb.h
  • lines changed 2, context: html, text, full: html, text
    3e42e5911fd90bf74e8733bb30db5687886fdb73 Mon Oct 10 14:07:29 2016 -0700
    first pass at utility to convert hub metadata to a RA file
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    2d208dcc8ef34de7627709e16e6f70f6fe6a8b8c Mon Oct 17 10:20:56 2016 -0700
    New version number v340
    
• src/hg/lib/mdb.c
  • lines changed 1, context: html, text, full: html, text
    3e42e5911fd90bf74e8733bb30db5687886fdb73 Mon Oct 10 14:07:29 2016 -0700
    first pass at utility to convert hub metadata to a RA file
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 35, context: html, text, full: html, text
    51578c144572d37b2cf5af75c9d6a96ee5539328 Mon Oct 10 13:48:37 2016 -0700
    re-do hgPal downloads for hg19
    
  • lines changed 18, context: html, text, full: html, text
    a2658279f3ea3862ba38e92eb282b6c36e4dff3c Fri Oct 14 11:26:21 2016 -0700
    Build /gbdb/hg{19,38}/vai/snp147.bed4.bb so hgVai queries that include rs# ID aren't horribly slow. This should probably be incorporated into the dbSNP pipeline. refs #18222
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 18, context: html, text, full: html, text
    a2658279f3ea3862ba38e92eb282b6c36e4dff3c Fri Oct 14 11:26:21 2016 -0700
    Build /gbdb/hg{19,38}/vai/snp147.bed4.bb so hgVai queries that include rs# ID aren't horribly slow. This should probably be incorporated into the dbSNP pipeline. refs #18222
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 5, context: html, text, full: html, text
    8b12505da5d4d2926495c460832229dfaf17efb2 Wed Oct 12 09:06:48 2016 -0700
    Turning on GenBank updates for chlSab2, gorGor5, and panTro5
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 5, context: html, text, full: html, text
    febdfbb8c7c452a0fc7ae426b4e56d2b76474915 Fri Oct 14 14:13:26 2016 -0700
    turning on rr genbank updates for gorGor5 panTro5 chlSab2
    
• src/hg/makeDb/trackDb/human/omimAvSnp.html
  • lines changed 3, context: html, text, full: html, text
    ccd80773e581e1b6977015459ab4966d0e1a6124 Tue Oct 11 04:55:08 2016 -0700
    OMIM Allele track docs now correctly name snp track used for intersection,
    also correctly describes our linkouts, refs #16796
    
  • lines changed 3, context: html, text, full: html, text
    371bf107a7e43976d378221aa4d16fa347bb3981 Tue Oct 11 05:53:23 2016 -0700
    OMIM Alleles now has more linkouts in the documentation, refs #16796
    
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 270, context: html, text, full: html, text
    1eb2b35c704cc487635b4c8539a2d84d8da2e450 Mon Oct 10 17:07:48 2016 -0700
    adding v86 definitions refs #18216
    
• src/hg/utils/hubToMetaRa/hubToMetaRa.c
  • lines changed 161, context: html, text, full: html, text
    3e42e5911fd90bf74e8733bb30db5687886fdb73 Mon Oct 10 14:07:29 2016 -0700
    first pass at utility to convert hub metadata to a RA file
    
• src/hg/utils/hubToMetaRa/makefile
  • lines changed 3, context: html, text, full: html, text
    3e42e5911fd90bf74e8733bb30db5687886fdb73 Mon Oct 10 14:07:29 2016 -0700
    first pass at utility to convert hub metadata to a RA file
    
• src/lib/htmshell.c
  • lines changed 21, context: html, text, full: html, text
    fc290bc3a314d67cc1d9b354c2a670142b386536 Mon Oct 10 13:23:12 2016 -0700
    Cleaning out old stuff. In the past TimD had tried to encode newlines in htmlEncode. He was really trying to encode them in html attributes, especially the TITLE attribute in hgTracks/imageV2.c. Since we now have a proper attribute encoder that works for all characters, and it works with modern Firefox, the special handling is no longer needed.
    
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    254a0a6357dce9f6659ab9f9dd41553a881a0987 Tue Oct 11 09:22:56 2016 -0700
    As Belinda Giardine pointed out, VCF genotype indexes should be initialized in case they somehow slip through parsing. refs #18219
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    aca4c5d59cbfb19d89ff21dbf37e36d1617d45c1 Mon Oct 17 10:08:21 2016 -0700
    v340 final build refs #18175
    

• lines changed: 1316
• files changed: 35