All File Changes

v332_base to v333_preview (2016-05-02 to 2016-05-09) v333

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    76fd947d26f877412e2d6cf4cb8bd2f1189232c4 Mon May 2 14:44:47 2016 -0700
    editing hg.conf for new gateway page tree menu to display, refs #15277
    
  • lines changed 3, context: html, text, full: html, text
    1b1e5f5fdfa4aad1f3e67eca0e530ca2fb0338b4 Fri May 6 10:37:08 2016 -0700
    Adding survey changes to hgwbeta.hg.conf refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    4f01dece0ff192bcf04f63b8077742320e2e82ad Sun May 8 01:11:29 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    4f01dece0ff192bcf04f63b8077742320e2e82ad Sun May 8 01:11:29 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 8, context: html, text, full: html, text
    4f01dece0ff192bcf04f63b8077742320e2e82ad Sun May 8 01:11:29 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 3, context: html, text, full: html, text
    c8a3f2f43eb4f12007408a767bce133ab98bcfde Mon May 2 14:07:34 2016 -0700
    gBiB v332 now using new gateway phylo tree image refs #17202
    
• src/hg/bedOrBlocks/bedOrBlocks.c
  • lines changed 12, context: html, text, full: html, text
    1e2e00c67a11edf9693b019c75596e2158723ba0 Mon May 2 15:40:57 2016 -0700
    add a mode to bedOrBlocks to cluster based on name, use this mode to
    build the pFam track on the new hg38 knownGene
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 2, context: html, text, full: html, text
    cdde503aec0a7ee60d1df0064f6a2b1a4641895e Wed Apr 27 16:15:23 2016 -0700
    Adding a little check on range of files.
    
  • lines changed 14, context: html, text, full: html, text
    75d0cbbdf2917d32627f4b7852537624f5ec455c Wed May 4 17:24:14 2016 -0700
    Cutting out piece of code that integrates both manifest and meta tags into a searchable cgiParsedVars list into a function that is shared with cdwSubmit as well as the original cdwMakeValidFile.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 2, context: html, text, full: html, text
    aa51926e702f65eca7e9abfb12566c5f0cde2a67 Wed May 4 17:21:14 2016 -0700
    Adding lane field to cdwValidFile.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    75d0cbbdf2917d32627f4b7852537624f5ec455c Wed May 4 17:24:14 2016 -0700
    Cutting out piece of code that integrates both manifest and meta tags into a searchable cgiParsedVars list into a function that is shared with cdwSubmit as well as the original cdwMakeValidFile.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    aa51926e702f65eca7e9abfb12566c5f0cde2a67 Wed May 4 17:21:14 2016 -0700
    Adding lane field to cdwValidFile.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 13, context: html, text, full: html, text
    aa51926e702f65eca7e9abfb12566c5f0cde2a67 Wed May 4 17:21:14 2016 -0700
    Adding lane field to cdwValidFile.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 1, context: html, text, full: html, text
    aa51926e702f65eca7e9abfb12566c5f0cde2a67 Wed May 4 17:21:14 2016 -0700
    Adding lane field to cdwValidFile.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 26, context: html, text, full: html, text
    75d0cbbdf2917d32627f4b7852537624f5ec455c Wed May 4 17:24:14 2016 -0700
    Cutting out piece of code that integrates both manifest and meta tags into a searchable cgiParsedVars list into a function that is shared with cdwSubmit as well as the original cdwMakeValidFile.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 2, context: html, text, full: html, text
    f1875606a1aab2f89f0e49b6d7271efbb86d7b79 Wed May 4 15:31:31 2016 -0700
    Adding average_insert_size and lane tags.
    
  • lines changed 1, context: html, text, full: html, text
    a729bb443352c4ec5501e0a18e720bdcb3366a05 Wed May 4 17:25:04 2016 -0700
    Adding pcr_cycles tag.
    
• src/hg/cirm/cdw/wrangle/addToStepTables/addToStepTables
  • lines changed 164, context: html, text, full: html, text
    d4f2511d5385baf26c03829924decf7a88bbb3ea Wed May 4 11:58:39 2016 -0700
    Renaming the addToStepTables script to maniMani, refs #16113
    
• src/hg/cirm/cdw/wrangle/addToStepTables/makefile
  • lines changed 6, context: html, text, full: html, text
    d4f2511d5385baf26c03829924decf7a88bbb3ea Wed May 4 11:58:39 2016 -0700
    Renaming the addToStepTables script to maniMani, refs #16113
    
• src/hg/cirm/cdw/wrangle/maniMani/makefile
  • lines changed 6, context: html, text, full: html, text
    d4f2511d5385baf26c03829924decf7a88bbb3ea Wed May 4 11:58:39 2016 -0700
    Renaming the addToStepTables script to maniMani, refs #16113
    
• src/hg/cirm/cdw/wrangle/maniMani/maniMani
  • lines changed 162, context: html, text, full: html, text
    d4f2511d5385baf26c03829924decf7a88bbb3ea Wed May 4 11:58:39 2016 -0700
    Renaming the addToStepTables script to maniMani, refs #16113
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 5, context: html, text, full: html, text
    da1f0d67fe492b997b07bbebe6e5f4a86170331b Wed May 4 10:07:18 2016 -0700
    Same as in hgGateway (d30337d4), I forgot to initialize oldVars (thanks Hiram for noticing!) and also wasn't using getDbGenomeClade which handles position reset when db changes. refs #17267#note-5.
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    d30337d436a490a59698f716c0defabe3f40035a Tue May 3 13:05:38 2016 -0700
    hgGateway wasn't initializing oldVars, so switching db via CGI led to keeping old position -- thanks Brian L! refs #15277 note-257.
    
• src/hg/hgGene/alleles.c
  • lines changed 39, context: html, text, full: html, text
    58f241185a4522bb0dd6bac6df5b1abe4f5d6a4f Wed May 4 13:22:25 2016 -0700
    Shift alleles section code from exists to print routine to allow hide of section to speed up hgGene which is slow on hg19. Part of perf improvements when adding GTEx to hgGene. refs #17244
    
• src/hg/hgGene/gtex.c
  • lines changed 62, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 4, context: html, text, full: html, text
    c32415cfb3e0d34c6c21ad9b10dbd66c7ef2b76b Mon May 2 10:44:28 2016 -0700
    Add link to browser with GTEX track on to hgGene GTEX section. refs #17244
    
  • lines changed 29, context: html, text, full: html, text
    c4da827b5b232b002a32e2ec07cdb6b2494df4e4 Mon May 2 14:23:26 2016 -0700
    Add highest and total median expression info to section panel. refs #17244
    
  • lines changed 43, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 35, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
  • lines changed 21, context: html, text, full: html, text
    ddafb30c2f0d5489f4a56c280f56fabf0b08c161 Wed May 4 12:45:18 2016 -0700
    Add default visibility feature to hgGene sections. Setting 'visiblity hide' in section.ra will cause section to be collapsed as default. Using this to set microarray sections to default closed when GTEx data is present (perf boost). refs #17244
    
• src/hg/hgGene/hgGene.h
  • lines changed 3, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 2, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
• src/hg/hgGene/hgGeneData/Human/hg19/section.ra
  • lines changed 9, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 2, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
  • lines changed 6, context: html, text, full: html, text
    ddafb30c2f0d5489f4a56c280f56fabf0b08c161 Wed May 4 12:45:18 2016 -0700
    Add default visibility feature to hgGene sections. Setting 'visiblity hide' in section.ra will cause section to be collapsed as default. Using this to set microarray sections to default closed when GTEx data is present (perf boost). refs #17244
    
  • lines changed 1, context: html, text, full: html, text
    c9f540c357130c039f10a9da275891a461b99cae Wed May 4 14:07:11 2016 -0700
    Set Gene Alleles section to default off. Saves 500-1000 msec. By request of JK. Part of perf improvements motivated by adding GTEx section. refs #17244
    
• src/hg/hgGene/hgGeneData/Human/hg38/section.ra
  • lines changed 7, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 2, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
  • lines changed 11, context: html, text, full: html, text
    ddafb30c2f0d5489f4a56c280f56fabf0b08c161 Wed May 4 12:45:18 2016 -0700
    Add default visibility feature to hgGene sections. Setting 'visiblity hide' in section.ra will cause section to be collapsed as default. Using this to set microarray sections to default closed when GTEx data is present (perf boost). refs #17244
    
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 10, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
• src/hg/hgGene/hgGeneData/section.ra
  • lines changed 1, context: html, text, full: html, text
    6eb7b642e4d1286b4662ea3d527a9bc09b17db70 Wed May 4 10:53:50 2016 -0700
    Performance work: Add measureTiming support. Also, restructure GTEx to move heavy lifting to print routine so closing section will save time. Also, a few label changes for expression sections. refs #17244
    
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 5, context: html, text, full: html, text
    da1f0d67fe492b997b07bbebe6e5f4a86170331b Wed May 4 10:07:18 2016 -0700
    Same as in hgGateway (d30337d4), I forgot to initialize oldVars (thanks Hiram for noticing!) and also wasn't using getDbGenomeClade which handles position reset when db changes. refs #17267#note-5.
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 1, context: html, text, full: html, text
    d446cddda15c625da719f26d1567769e9ea5356a Tue May 3 17:55:36 2016 -0700
    fixing typo in usage screen.
    
• src/hg/hgTracks/coverageTrack.c
  • lines changed 22, context: html, text, full: html, text
    76aea2be605116a4ca247f4a3895650376b301dd Thu May 5 12:58:24 2016 -0700
    Adding comment to document a problem with right-click on clonePos which we understand, but are not going to fix at this time.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    7ab16d909d9bbd6b55565c87f7ad7b645caa90a2 Thu May 5 19:54:36 2016 -0700
    Tweak the new darkerLabels setting to further darken extra pale colors.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    4b83e0cd3c28ecda13879b2c4c4a5904b8aa95ba Thu May 5 13:44:28 2016 -0700
    Speeding up ORegAnno load and draw, refs #15957
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    cde03431a6a4f1f6eb256b3e0c2521c2dd77869b Wed May 4 14:16:12 2016 -0700
    Oops sql injection fixes.
    
  • lines changed 24, context: html, text, full: html, text
    4b83e0cd3c28ecda13879b2c4c4a5904b8aa95ba Thu May 5 13:44:28 2016 -0700
    Speeding up ORegAnno load and draw, refs #15957
    
• src/hg/hgc/gencodeClick.c
  • lines changed 3, context: html, text, full: html, text
    cde03431a6a4f1f6eb256b3e0c2521c2dd77869b Wed May 4 14:16:12 2016 -0700
    Oops sql injection fixes.
    
• src/hg/hgc/gtexClick.c
  • lines changed 32, context: html, text, full: html, text
    b46d372807d2ffc6fd3d03ec2ad71dd72a361672 Thu Apr 28 11:15:14 2016 -0700
    Refactor GTEx boxplot code in preparation for moving to library for shared use with hgGene
    
  • lines changed 146, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
  • lines changed 11, context: html, text, full: html, text
    b3bbb2830441deb68f6645938db234d0ce7f170d Thu Apr 28 13:17:13 2016 -0700
    Cleanup for readability.
    
  • lines changed 2, context: html, text, full: html, text
    2226ef649b0fbb80ce771caeda16c71ccc290eac Mon May 2 10:46:16 2016 -0700
    Add link to browser with GTEX track on to hgGene GTEX section. refs #17244
    
  • lines changed 6, context: html, text, full: html, text
    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    cde03431a6a4f1f6eb256b3e0c2521c2dd77869b Wed May 4 14:16:12 2016 -0700
    Oops sql injection fixes.
    
  • lines changed 14, context: html, text, full: html, text
    699bed02317b5aa434c08fd446099623c4f7f54a Thu May 5 14:51:21 2016 -0700
    working on bigMaf doc
    
  • lines changed 3, context: html, text, full: html, text
    48607395c5be6a047d54429310deeada24198b36 Fri May 6 15:57:51 2016 -0700
    some tweaks to get bigMaf custom tracks to work
    
  • lines changed 3, context: html, text, full: html, text
    6a74b39270290c9a2718459dba60e6b2587c2e76 Fri May 6 18:22:31 2016 -0700
    various changes to support and doc bigChain custom tracks
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 69, context: html, text, full: html, text
    6a74b39270290c9a2718459dba60e6b2587c2e76 Fri May 6 18:22:31 2016 -0700
    various changes to support and doc bigChain custom tracks
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 88, context: html, text, full: html, text
    699bed02317b5aa434c08fd446099623c4f7f54a Thu May 5 14:51:21 2016 -0700
    working on bigMaf doc
    
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 66, context: html, text, full: html, text
    adc23952f6d63fea678296157f76ff84afc98d53 Wed May 4 14:43:49 2016 -0700
    some updates the bigPsl.html page
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 37, context: html, text, full: html, text
    a08239e335e6fd9b8d5f4162ac03e05e055a11e3 Fri May 6 11:48:15 2016 -0700
    Updating Session Gallery TroubleShooting refs #17257 #14724
    
• src/hg/htdocs/images/phylo/cavPor3.5way.png
  • lines changed 0, context: html, text, full: html, text
    033b8ed0e57429271ce63c0e781d75df5a958a0a Thu May 5 15:19:44 2016 -0700
    5-way phylo tree for cavPor3 refs #17180
    
  • lines changed 0, context: html, text, full: html, text
    7276e8318a5765c41ca1183ac4941f39f910ea51 Thu May 5 15:30:53 2016 -0700
    incorrect name for 5way.png
    
• src/hg/htdocs/images/phylo/cavPor3_5way.png
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    b47d3a1cba5a433a2b145e1021ccb3f52deb2ae1 Thu May 5 15:25:55 2016 -0700
    5-way phylo tree for cavPor3 refs #17180
    
• src/hg/htdocs/images/phylo/galVar1_5way.png
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    9d85b4c0cb35e2be8b1b41277d7d5a7e1d79aaa3 Tue May 3 12:48:49 2016 -0700
    5-way phylo tree for Malayan flying lemur refs #17180
    
• src/hg/htdocs/images/sneakPeekGateway.png
  • lines changed 0, context: html, text, full: html, text
    caedca93dc80fe382f961234c1bd21433347f3ac Thu May 5 13:45:20 2016 -0700
    Adding image for Google Group pre-announcement to new gateway page, refs # 15277
    
• src/hg/htdocs/indexNews.html
  • lines changed 21, context: html, text, full: html, text
    749365e6604752703aae059624cd948a25000fba Thu May 5 17:36:11 2016 -0700
    Adding temporary news on the homepage about the new gateway #15277
    
  • lines changed 1, context: html, text, full: html, text
    fe4959ce528118235d2fca5c45dfd6eab5d211dd Thu May 5 17:50:04 2016 -0700
    Adding name anchor to temporary news on the homepage about the new gateway #15277
    
  • lines changed 2, context: html, text, full: html, text
    fb173e3f29b6979c56950adfa4a6b79327a51aab Fri May 6 09:56:31 2016 -0700
    Adding missing line in news announcement refs #15277
    
• src/hg/htdocs/staff.html
  • lines changed 8, context: html, text, full: html, text
    3bdddcb0015ea550abeb2bcbfee1a7282d20003b Thu May 5 15:24:03 2016 -0700
    Adding Clayton to staff.html
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 3, context: html, text, full: html, text
    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    b46d372807d2ffc6fd3d03ec2ad71dd72a361672 Thu Apr 28 11:15:14 2016 -0700
    Refactor GTEx boxplot code in preparation for moving to library for shared use with hgGene
    
• src/hg/inc/gtexTissue.h
  • lines changed 3, context: html, text, full: html, text
    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/inc/gtexUi.h
  • lines changed 9, context: html, text, full: html, text
    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
• src/hg/inc/oreganno.h
  • lines changed 5, context: html, text, full: html, text
    4b83e0cd3c28ecda13879b2c4c4a5904b8aa95ba Thu May 5 13:44:28 2016 -0700
    Speeding up ORegAnno load and draw, refs #15957
    
• src/hg/lib/chainNetDbLoad.c
  • lines changed 1, context: html, text, full: html, text
    6a74b39270290c9a2718459dba60e6b2587c2e76 Fri May 6 18:22:31 2016 -0700
    various changes to support and doc bigChain custom tracks
    
• src/hg/lib/customFactory.c
  • lines changed 38, context: html, text, full: html, text
    699bed02317b5aa434c08fd446099623c4f7f54a Thu May 5 14:51:21 2016 -0700
    working on bigMaf doc
    
  • lines changed 18, context: html, text, full: html, text
    6a74b39270290c9a2718459dba60e6b2587c2e76 Fri May 6 18:22:31 2016 -0700
    various changes to support and doc bigChain custom tracks
    
• src/hg/lib/gtexBoxplot.c
  • lines changed 160, context: html, text, full: html, text
    ba9c4b8c144df33072d58154549b7cf531d15bde Tue May 3 09:14:22 2016 -0700
    Libifying GTEx boxplot for use by hgGene (as well as hgc). refs #17244
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 18, context: html, text, full: html, text
    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/lib/gtexInfo.c
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    b46d372807d2ffc6fd3d03ec2ad71dd72a361672 Thu Apr 28 11:15:14 2016 -0700
    Refactor GTEx boxplot code in preparation for moving to library for shared use with hgGene
    
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    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/lib/gtexTissue.c
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    114bd9cc108feeb8b20ad0b98b35454ea3fde8e0 Mon May 2 11:45:50 2016 -0700
    Add details page info to show highest expressed tissue with scores. refs #17244
    
• src/hg/lib/gtexUi.c
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    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
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    c32415cfb3e0d34c6c21ad9b10dbd66c7ef2b76b Mon May 2 10:44:28 2016 -0700
    Add link to browser with GTEX track on to hgGene GTEX section. refs #17244
    
• src/hg/lib/hgFind.c
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    c0e3e877d69f282dc5a445e8747cb71cf565de1d Mon May 2 14:25:49 2016 -0700
    Adding back some functionality lost in fadb7a07e: fuzzy search for cytoBand terms that are either more specific or more general than the band names in cytoBands. refs #17253
    
• src/hg/lib/makefile
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    000226be7ecaa7674455d3968af3590ff2a047b3 Thu Apr 28 13:13:40 2016 -0700
    Add GTEx gene expression boxplot to hg38 and hg19 hgGene pages. Remove old GTEx link. refs #17244
    
• src/hg/lib/omim2gene.as
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    77addc5d489ad0e6d9828b58390f13298a0beda4 Tue May 3 08:43:05 2016 -0700
    Fixing autoSql comment syntax error.
    
• src/hg/lib/oreganno.c
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    4b83e0cd3c28ecda13879b2c4c4a5904b8aa95ba Thu May 5 13:44:28 2016 -0700
    Speeding up ORegAnno load and draw, refs #15957
    
• src/hg/lib/tests/genePredTests.mk
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    051abf9c3ec8f839056f03e43bfa8a02fde1adda Sat May 7 08:46:01 2016 -0700
    use hg15 as compatibility database test, since hg16.refGene changed
    
• src/hg/makeDb/doc/cavPor3.txt
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    fb489d6bfc25b542c4cca14e61e38c3eb1353298 Thu May 5 15:29:45 2016 -0700
    multiz5way frames done refs #17180
    
• src/hg/makeDb/doc/galVar1/lastzRuns.txt
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    aa8251bd333deaa55fff02b1df38775160e0ab58 Tue May 3 14:01:27 2016 -0700
    5-way multiz done refs #17180
    
• src/hg/makeDb/doc/galVar1/multiz5way.txt
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    aa8251bd333deaa55fff02b1df38775160e0ab58 Tue May 3 14:01:27 2016 -0700
    5-way multiz done refs #17180
    
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    c925f0b56667c9987c4c16f3833f78b15d248d6e Thu May 5 10:02:29 2016 -0700
    gap annotation done refs #17180
    
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    329d0f2f0ebe4a6a826c4db6bfdd60392e416442 Thu May 5 15:29:13 2016 -0700
    frames done refs #17180
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    5399f1fc35a8da92c078bf4753235fab3b02c268 Tue May 3 14:57:18 2016 -0700
    lastz run on galVar1 refs #17180
    
• src/hg/makeDb/doc/mm10.txt
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    d390a45c2e67726a563a7db85c3139793c7cc05c Tue May 3 12:19:31 2016 -0700
    lastz run to galGal1 refs #17180
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
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    1e2e00c67a11edf9693b019c75596e2158723ba0 Mon May 2 15:40:57 2016 -0700
    add a mode to bedOrBlocks to cluster based on name, use this mode to
    build the pFam track on the new hg38 knownGene
    
• src/hg/makeDb/trackDb/fosEndPairs.html
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    5b66322256b5c8b99bdcd59e194b95437c82f4c2 Tue May 3 19:36:40 2016 -0700
    Adding note to whereabouts of Fosmid End track on hg19,19 refs #15523
    
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra
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    1f78713caba1393510be4f29850bc395074f0492 Tue May 3 15:18:59 2016 -0700
    adding multiz 5-way alignment track refs #17180
    
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    3d953a2264e19f75f2ff2f26efb04ef9ddf31830 Tue May 3 15:42:04 2016 -0700
    no frames yet refs #17180
    
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    798885291382ef8378541aca4da24d307b05f02b Thu May 5 15:12:26 2016 -0700
    turning on frames feature refs #17180
    
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra
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    1f78713caba1393510be4f29850bc395074f0492 Tue May 3 15:18:59 2016 -0700
    adding multiz 5-way alignment track refs #17180
    
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.5way.ra
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    0828e268f41122eb4a3d48b22a823b9151c37fdb Tue May 3 15:51:27 2016 -0700
    adding 5-way multiz refs #17180
    
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    798885291382ef8378541aca4da24d307b05f02b Thu May 5 15:12:26 2016 -0700
    turning on frames feature refs #17180
    
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
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    0828e268f41122eb4a3d48b22a823b9151c37fdb Tue May 3 15:51:27 2016 -0700
    adding 5-way multiz refs #17180
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    08085aeb73b03fd0156311c3932b907b47e7fa9f Thu May 5 14:09:23 2016 -0700
    Changing location of span tag based on CR, refs #17254
    
• src/hg/makeDb/trackDb/rhesus/rheMac8/description.html
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    938f80b8b54787bc339dd08deb24931906858a0e Mon May 2 15:09:12 2016 -0700
    Fixing references formatting, refs #16744
    
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    bfdfcba26e9acd9d1e7eb771c52e8ad624ee56f2 Mon May 2 16:04:27 2016 -0700
    Minor edit & cleaning code line wraps
    
• src/hg/mouseStuff/chainCleaner/NetFilterNonNested.perl
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    fbdd2992e994a348c9b2d14922f872d85edc66f7 Mon May 9 09:58:19 2016 -0700
    adding chainCleaner code from Michael Hiller refs #17286
    
• src/hg/mouseStuff/chainCleaner/chainCleaner.c
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    fbdd2992e994a348c9b2d14922f872d85edc66f7 Mon May 9 09:58:19 2016 -0700
    adding chainCleaner code from Michael Hiller refs #17286
    
• src/hg/mouseStuff/chainCleaner/makefile
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    fbdd2992e994a348c9b2d14922f872d85edc66f7 Mon May 9 09:58:19 2016 -0700
    adding chainCleaner code from Michael Hiller refs #17286
    
• src/hg/utils/automation/accRsu.pl
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    18e1d22e10b537ad3813c365bd4cae8c59f59d87 Thu May 5 12:31:53 2016 -0700
    handle the case of no curated genes and sparse/missing description text refs #13673
    
• src/hg/utils/automation/doNcbiRefSeq.pl
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    18e1d22e10b537ad3813c365bd4cae8c59f59d87 Thu May 5 12:31:53 2016 -0700
    handle the case of no curated genes and sparse/missing description text refs #13673
    
• src/inc/basicBed.h
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    1e2e00c67a11edf9693b019c75596e2158723ba0 Mon May 2 15:40:57 2016 -0700
    add a mode to bedOrBlocks to cluster based on name, use this mode to
    build the pFam track on the new hg38 knownGene
    
• src/inc/cheapcgi.h
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    873ee852526ee64094fbc7ac2078820b7856c00e Wed May 4 17:20:12 2016 -0700
    Adding function to free a whole list of cgiParsedVars.
    
• src/lib/basicBed.c
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    1e2e00c67a11edf9693b019c75596e2158723ba0 Mon May 2 15:40:57 2016 -0700
    add a mode to bedOrBlocks to cluster based on name, use this mode to
    build the pFam track on the new hg38 knownGene
    
• src/lib/cheapcgi.c
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    873ee852526ee64094fbc7ac2078820b7856c00e Wed May 4 17:20:12 2016 -0700
    Adding function to free a whole list of cgiParsedVars.
    
• src/utils/qa/weeklybld/boxRelease.csh
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    4d05ee12364aabb2ea43c2751538ef834001d77b Tue May 3 16:20:18 2016 -0700
    correct grep command to find running boxes refs #17202
    
• src/utils/qa/weeklybld/buildEnv.csh
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    b05b7e03048f62c7a326227876ca7153843f08fe Mon May 9 10:08:59 2016 -0700
    v333 preview1 refs #17287
    

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