All File Changes

v338_preview2 to v338_base (2016-08-29 to 2016-09-06) v338

• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 12, context: html, text, full: html, text
    3a6492f1757fb908cc1d4f930c1f0100957cfe13 Fri Sep 2 22:57:24 2016 -0700
    adding dummy html tags to make e cdwSummary html pass Jim's validator
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.h
  • lines changed 44, context: html, text, full: html, text
    a15689d923ef1d7c5def464712d5c6e96cb9822c Tue Aug 30 16:55:50 2016 -0700
    Cleaning up the prod page and fixing some minor bugs, refs #17870
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 113, context: html, text, full: html, text
    a15689d923ef1d7c5def464712d5c6e96cb9822c Tue Aug 30 16:55:50 2016 -0700
    Cleaning up the prod page and fixing some minor bugs, refs #17870
    
  • lines changed 23, context: html, text, full: html, text
    0e15199f0fab53acde6f023a9174826783ad9205 Tue Aug 30 17:52:39 2016 -0700
    Refactoring the browse datasets tab for speed, refs #17870
    
• src/hg/genePredToFakePsl/genePredToFakePsl.c
  • lines changed 24, context: html, text, full: html, text
    b642fe3045bbc0df86e56957d61d7851fc5a127c Tue Aug 30 14:10:06 2016 -0700
    add qSizes argument so the qSizes can be adjusted to their true RNA size refs #13673
    
• src/hg/hgGene/domains.c
  • lines changed 2, context: html, text, full: html, text
    330b714d5af720037262c6f8b7bb66598076fd03 Mon Aug 29 16:51:12 2016 -0700
    Fixing URL to Pfam Domains page from hgGene, refs #15342
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 10, context: html, text, full: html, text
    11ae1f3a602299a281491e5191e8dbc0ee143648 Fri Sep 2 09:24:31 2016 -0700
    hgIntegrator was missing the now-required call to initGenbankTableNames after establishing db (thx Brian L). refs #15071 note-79
    
• src/hg/hgTables/identifiers.c
  • lines changed 2, context: html, text, full: html, text
    06598725532a350f0a2aee1c5fe67cfd338e9b5b Wed Aug 31 13:26:17 2016 -0700
    some fixes for NCBI RefSeq track
    
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    06598725532a350f0a2aee1c5fe67cfd338e9b5b Wed Aug 31 13:26:17 2016 -0700
    some fixes for NCBI RefSeq track
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    4867f2218a18f18c50b2ec527be60ee5a63b8a81 Wed Aug 31 12:11:12 2016 -0700
    Static doc edits for new chicken genome, refs #17168
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    4867f2218a18f18c50b2ec527be60ee5a63b8a81 Wed Aug 31 12:11:12 2016 -0700
    Static doc edits for new chicken genome, refs #17168
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    c04e4f6c04b5ce49b16ba35d81e1533edafe5368 Tue Aug 30 14:06:55 2016 -0700
    Announcing gtex ase public hub, refs #17885
    
  • lines changed 22, context: html, text, full: html, text
    4867f2218a18f18c50b2ec527be60ee5a63b8a81 Wed Aug 31 12:11:12 2016 -0700
    Static doc edits for new chicken genome, refs #17168
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 7, context: html, text, full: html, text
    449ae667c0139b927c677d8da0145322a50fea26 Fri Sep 2 10:24:23 2016 -0700
    adding a publication from Max to pubs.html
    
• src/hg/htdocs/indexNews.html
  • lines changed 10, context: html, text, full: html, text
    c04e4f6c04b5ce49b16ba35d81e1533edafe5368 Tue Aug 30 14:06:55 2016 -0700
    Announcing gtex ase public hub, refs #17885
    
  • lines changed 13, context: html, text, full: html, text
    4867f2218a18f18c50b2ec527be60ee5a63b8a81 Wed Aug 31 12:11:12 2016 -0700
    Static doc edits for new chicken genome, refs #17168
    
• src/hg/htdocs/staff.html
  • lines changed 9, context: html, text, full: html, text
    dbaab6c7cb0ba490d722bf51a06f0b2b61b3aada Mon Aug 29 14:18:10 2016 -0700
    Added Jairo to Engineering and Management Staff, and moved Gary to Alumni section.
    
  • lines changed 8, context: html, text, full: html, text
    7995da04e079405afaec7464f30ce9cb58ff8a48 Mon Aug 29 14:35:50 2016 -0700
    added Chris V and Haifeng to staff page
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    840623808e1ddb54e8a5ccbf34136fb4a767c75c Tue Sep 6 10:05:57 2016 -0700
    New version number v338
    
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    dadfd3365009b4b81125c46aad7ad2d0b3c69671 Wed Aug 31 09:55:03 2016 -0700
    fix problem in support for composites in hgTrackUi
    
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    a3493ed2ff9a01552e8fe05540bd88b39541879d Fri Sep 2 10:33:51 2016 -0700
    Expand pseudo-HGVS regex to accept p. after gene name.
    
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    3aab1fb985b30c5750b241adc4d2e1cc2402b365 Mon Aug 29 15:05:39 2016 -0700
    Adding cloneString to avoid trouble in case anybody ever frees a track hub chromInfo list.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 58, context: html, text, full: html, text
    0f0f8fa62ea401a56bd29a2326cd91b35577145b Mon Aug 29 14:07:35 2016 -0700
    liftOver to balAcu1 per user request refs #17919
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    996e5cc86b8524d5c07fb31eb4f4a1f449d1e849 Tue Aug 30 09:16:09 2016 -0700
    Turning on Genbank updates for galGal5 on beta, refs #17168
    
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 8, context: html, text, full: html, text
    f8f10da56b32327eb6d549889ed80f301b85ade9 Thu Sep 1 08:09:11 2016 -0700
    more pointless work to support the Genbank pipeline ;-)
    
  • lines changed 1080, context: html, text, full: html, text
    0ef9d08ee96409fcea948a950c4712e199a1b6c6 Mon Sep 5 19:39:42 2016 -0700
    more stuff that I have to pay attention to so I can ignore it.
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    d717d73e1951e1ac3ee20c67cdb9957876d09c43 Tue Aug 30 13:27:50 2016 -0700
    Turning on genbank updates on rr for galGal5, refs #17168
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    216d45a09f3d3fdc5973d1d6259b5819a636716e Thu Sep 1 10:58:22 2016 -0700
    Lowering minCheck for kgGeneSymbol to make omim geneMap happy, refs #18012
    
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 1, context: html, text, full: html, text
    2f9fe3c15f648a958c8474e3a870d0913e44223b Wed Aug 31 09:36:59 2016 -0700
    Adjusting release tags for galGal5 chain/net tracks in hg38 and mm10, refs #17168
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    2f9fe3c15f648a958c8474e3a870d0913e44223b Wed Aug 31 09:36:59 2016 -0700
    Adjusting release tags for galGal5 chain/net tracks in hg38 and mm10, refs #17168
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    06598725532a350f0a2aee1c5fe67cfd338e9b5b Wed Aug 31 13:26:17 2016 -0700
    some fixes for NCBI RefSeq track
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    06598725532a350f0a2aee1c5fe67cfd338e9b5b Wed Aug 31 13:26:17 2016 -0700
    some fixes for NCBI RefSeq track
    
• src/hg/near/hgExpDistance/hgMaxExp.c
  • lines changed 8, context: html, text, full: html, text
    60da58a934d9407e391372b9048340ddcb787d2d Wed Aug 31 09:20:30 2016 -0700
    Add min
    
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
  • lines changed 1, context: html, text, full: html, text
    465b7d50e5dcd04581ff817f1401022d04d687f6 Mon Aug 29 16:16:39 2016 -0700
    Leave gene sorter column defaults as is until GTEx tables are pushed. refs #17288
    
  • lines changed 27, context: html, text, full: html, text
    9a5624d4c52d81abdd5f1e5ebc67458e54a95088 Wed Aug 31 09:10:26 2016 -0700
    Update config, in prep for release of tables. Set GTEx to default on. Remove GNF Atlas 1. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/gtex.html
  • lines changed 1, context: html, text, full: html, text
    a76cc31a5626ec419fce338fa63e3b40b7115a51 Wed Aug 31 14:54:56 2016 -0700
    Improve link to GTEx track description, as per QA review. refs #17288
    
• src/hg/near/hgNear/hgNearData/orderDb.ra
  • lines changed 5, context: html, text, full: html, text
    9a5624d4c52d81abdd5f1e5ebc67458e54a95088 Wed Aug 31 09:10:26 2016 -0700
    Update config, in prep for release of tables. Set GTEx to default on. Remove GNF Atlas 1. refs #17288
    
• src/hg/near/hgNear/knownGene.c
  • lines changed 4, context: html, text, full: html, text
    c0774f4be7434a91104ef07668fb639d7642df84 Tue Aug 30 09:56:39 2016 -0700
    Fix buffer overflow. refs #18002
    
• src/hg/near/makeNear.doc
  • lines changed 20, context: html, text, full: html, text
    b59391a116347bd32c8d20f829abe3e75cf5cf51 Mon Aug 29 16:17:32 2016 -0700
    Finish hg38 GTEx in gene sorter. refs #17288
    
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 7, context: html, text, full: html, text
    63e70108d7261549b8385d6499c97c9e1ddc060d Tue Aug 30 14:15:49 2016 -0700
    now using qSizes on genePredToFakePsl refs #13673
    
• src/htslib/Makefile
  • lines changed 4, context: html, text, full: html, text
    e327f01b1a1919b6441797f4757d55d317bddf1c Wed Aug 31 17:17:55 2016 -0700
    some small tweaks in htslib to better incorporate it in the build
    
• src/htslib/cram/cram_io.c
  • lines changed 1, context: html, text, full: html, text
    e327f01b1a1919b6441797f4757d55d317bddf1c Wed Aug 31 17:17:55 2016 -0700
    some small tweaks in htslib to better incorporate it in the build
    
• src/htslib/cram/cram_stats.c
  • lines changed 2, context: html, text, full: html, text
    e327f01b1a1919b6441797f4757d55d317bddf1c Wed Aug 31 17:17:55 2016 -0700
    some small tweaks in htslib to better incorporate it in the build
    
• src/lib/htmshell.c
  • lines changed 12, context: html, text, full: html, text
    febe3b4030b731590c83b2843306f52b28ab792b Tue Aug 30 12:13:27 2016 -0700
    Improving comment accuracy, thanks Brian.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    2517b3a52d15b1ed792ac95f4053b2a3657bce38 Tue Sep 6 10:04:37 2016 -0700
    v338 final build refs #17934
    

• lines changed: 1602
• files changed: 45