All File Changes

v357_preview to v357_preview2 (2017-10-16 to 2017-10-23) v357

• .gitignore
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    9b2fadbb348edae6d5a39166a4f34d0cf6abefb6 Mon Oct 16 15:21:06 2017 -0700
    gitignore generated header file
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 2, context: html, text, full: html, text
    4917a38c21a998a5f9710bb99b6d6e53f354c722 Thu Oct 19 12:03:21 2017 -0700
    Only check overlap with the gap table if we are not checking the gap table. Only check unbridged gaps if explicitly asked
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 717, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
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    d1049074bc12250707523163499c0ac14f1b47f1 Tue Oct 17 14:36:58 2017 -0700
    Minor change to make page work in a new subdirectory, no redmine
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    c9fc90d8bf8acc97431f2a7fb33bbe08b8744ee5 Tue Oct 17 15:59:29 2017 -0700
    Making images work as part of a subdirectory. Adding links to institution websites.
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 454, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
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    d1049074bc12250707523163499c0ac14f1b47f1 Tue Oct 17 14:36:58 2017 -0700
    Minor change to make page work in a new subdirectory, no redmine
  • lines changed 4, context: html, text, full: html, text
    720477f77c52c2bbfa9a7e4ca866d8fde0df9e84 Tue Oct 17 15:22:11 2017 -0700
    Adding link to cescg publication page
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 259, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
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    d1049074bc12250707523163499c0ac14f1b47f1 Tue Oct 17 14:36:58 2017 -0700
    Minor change to make page work in a new subdirectory, no redmine
• src/hg/cirm/gateway/htdocs/cescgOrg.html
  • lines changed 717, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
• src/hg/cirm/gateway/htdocs/cescgPeople.html
  • lines changed 454, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
• src/hg/cirm/gateway/htdocs/cescgPubs.html
  • lines changed 259, context: html, text, full: html, text
    fb71f8becc5ce63dd9af44ce1818b2f8e7dc32aa Tue Oct 17 10:38:40 2017 -0700
    Moving cescg files into a subdirectory, no redmine
• src/hg/cirm/gateway/htdocs/footer.html
  • lines changed 7, context: html, text, full: html, text
    1022ad804b97d823a4afdf4380a0cd2525211099 Mon Oct 16 13:35:42 2017 -0700
    Minor changes to footer file to make it work when HTML files aren't at root level, adopted from Genome Browser code. First pass at making search box work; in short it doesn't work yet, but it's getting there. Also commiting new favicon for the SC Hub, adapted from SC Hub log Clay made, no redmine
  • lines changed 2, context: html, text, full: html, text
    72cda9bd11dd1b9eec45733b9031a1df1986439b Tue Oct 17 15:02:24 2017 -0700
    Minor changes to links in header and footer, no redmine
  • lines changed 1, context: html, text, full: html, text
    9d66133843779c1726c8e1a3fdba1c70260e2bcb Tue Oct 17 15:22:57 2017 -0700
    Minor change to footer to make link work when included on page in subdirectory
  • lines changed 3, context: html, text, full: html, text
    698277d02c531907080ddaa44062f3acbfaa14f7 Thu Oct 19 11:43:48 2017 -0700
    Making search box work in header. Minor changes to footer urls.
• src/hg/cirm/gateway/htdocs/header.html
  • lines changed 24, context: html, text, full: html, text
    1022ad804b97d823a4afdf4380a0cd2525211099 Mon Oct 16 13:35:42 2017 -0700
    Minor changes to footer file to make it work when HTML files aren't at root level, adopted from Genome Browser code. First pass at making search box work; in short it doesn't work yet, but it's getting there. Also commiting new favicon for the SC Hub, adapted from SC Hub log Clay made, no redmine
  • lines changed 3, context: html, text, full: html, text
    72cda9bd11dd1b9eec45733b9031a1df1986439b Tue Oct 17 15:02:24 2017 -0700
    Minor changes to links in header and footer, no redmine
  • lines changed 4, context: html, text, full: html, text
    efc0113fcb2e8f1eeb387d5ca2fbae65d6406c61 Wed Oct 18 14:23:28 2017 -0700
    Adding some stuff to define ROOT value in index file. Changing header to use relative links.
  • lines changed 12, context: html, text, full: html, text
    698277d02c531907080ddaa44062f3acbfaa14f7 Thu Oct 19 11:43:48 2017 -0700
    Making search box work in header. Minor changes to footer urls.
  • lines changed 6, context: html, text, full: html, text
    5ad0cdb80c6c325ead16681719b16312c8ee5ebf Fri Oct 20 10:42:41 2017 -0700
    Fixing links to work when included on a file in a subdirectory, refs #19778
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 69, context: html, text, full: html, text
    d4fbd7e1bec01a99d591631c2b7c49e9ca144ddc Mon Oct 16 13:56:32 2017 -0700
    Adding more to the help page, no redmine
  • lines changed 42, context: html, text, full: html, text
    741008bb54634fe39f700cb51b2a1410ea8647dd Tue Oct 17 14:38:54 2017 -0700
    Mostly whitespace changes. Moved privacy stuff to its own section, no redmine
• src/hg/cirm/gateway/htdocs/help/cirmFAQ.html
  • lines changed 103, context: html, text, full: html, text
    fc9f0553008a3888fe3407a6241f54f81a3852b8 Tue Oct 17 14:39:44 2017 -0700
    First pass at adding an FAQ page, no redmine
  • lines changed 3, context: html, text, full: html, text
    cb7cefd9157e8b08cb72a0503cb3a4853efafaf6 Tue Oct 17 15:04:18 2017 -0700
    Minor change to make page work as part of subdirectory, no redmine
• src/hg/cirm/gateway/htdocs/images/cirmInsulinCells.jpg
  • lines changed 0, context: html, text, full: html, text
    23a3c1b9e2be0bcc934d35e396b36cba5ff97ba4 Tue Oct 17 15:34:14 2017 -0700
    Adding CESCG description + vision from Salk/Stanford sites. Adding image to home page
• src/hg/cirm/gateway/htdocs/images/cirmSChubLogo.jpg
  • lines changed 4, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
  • lines changed 4, context: html, text, full: html, text
    e89d99c7b98182874435d716cf3162fc81bd618b Wed Oct 18 14:01:47 2017 -0700
    Removing old logo file that doesn't work; replaced it with one that does.
• src/hg/cirm/gateway/htdocs/images/cirmSChubLogo.png
  • lines changed 0, context: html, text, full: html, text
    e89d99c7b98182874435d716cf3162fc81bd618b Wed Oct 18 14:01:47 2017 -0700
    Removing old logo file that doesn't work; replaced it with one that does.
• src/hg/cirm/gateway/htdocs/images/genomicsInitiativeStructureCIRM.png
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/ludwigCancerResearchLogo.jpg
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/salkLogoBlue.jpg
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/schub.ico
  • lines changed 0, context: html, text, full: html, text
    1022ad804b97d823a4afdf4380a0cd2525211099 Mon Oct 16 13:35:42 2017 -0700
    Minor changes to footer file to make it work when HTML files aren't at root level, adopted from Genome Browser code. First pass at making search box work; in short it doesn't work yet, but it's getting there. Also commiting new favicon for the SC Hub, adapted from SC Hub log Clay made, no redmine
• src/hg/cirm/gateway/htdocs/images/scrippsResearchInstitute.jpg
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/stanfordUniversityStacked.png
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/ucscVertical.png
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/images/ucsdLogoBlueGold.png
  • lines changed 0, context: html, text, full: html, text
    00c483fb18b321b7cc0565ac3b4b82ff3c4333e8 Tue Oct 17 14:31:58 2017 -0700
    Committing images for CESCG participating institutions, no redmine
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 55, context: html, text, full: html, text
    23a3c1b9e2be0bcc934d35e396b36cba5ff97ba4 Tue Oct 17 15:34:14 2017 -0700
    Adding CESCG description + vision from Salk/Stanford sites. Adding image to home page
  • lines changed 1, context: html, text, full: html, text
    efc0113fcb2e8f1eeb387d5ca2fbae65d6406c61 Wed Oct 18 14:23:28 2017 -0700
    Adding some stuff to define ROOT value in index file. Changing header to use relative links.
• src/hg/cirm/gateway/htdocs/makefile
  • lines changed 23, context: html, text, full: html, text
    58f33b7bb119ec2c653c6b18ae4e0a80dc8ed5c5 Wed Oct 18 12:50:31 2017 -0700
    First commit of a makefile. Should in theory work across cirm machines, hgwdev-cirm, cirm.ucsc.edu, and cirm-01
  • lines changed 2, context: html, text, full: html, text
    609e2f9328c0759b30b75e10bf8b35e7065f8b9d Wed Oct 18 12:51:52 2017 -0700
    Removing some accidentally committed experimental lines
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 1, context: html, text, full: html, text
    2ceeb5a8438c6e56f3420b202f33cdc71d66020f Wed Oct 18 15:01:09 2017 -0700
    Adding ROOT definition to tools and projects page
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 62, context: html, text, full: html, text
    ebb04f3ade1df646a0c0c70d3856e7b7b5c98950 Mon Oct 16 13:50:39 2017 -0700
    Reworks to the Tools page, added section for Sample Psychic. Added my notes for how to improve page in future in HTML comments, no redmine
  • lines changed 1, context: html, text, full: html, text
    2ceeb5a8438c6e56f3420b202f33cdc71d66020f Wed Oct 18 15:01:09 2017 -0700
    Adding ROOT definition to tools and projects page
• src/hg/hgCollection/hgCollection.c
  • lines changed 5, context: html, text, full: html, text
    7a6949d256eb4329de0a6cc7e0c2ae0da35b6bf0 Fri Oct 20 14:05:15 2017 -0700
    add + and - icons in front of tracks to make it easier to copy them into a collection or delete them from a collection
• src/hg/hgCustom/hgCustom.c
  • lines changed 3, context: html, text, full: html, text
    208da7ba73e4a9a84a6427b41f8f456ae280ae9f Tue Oct 17 17:56:51 2017 -0700
    Fixing compile errors.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    c097b1414eb0dc077f2f126a0c21e755099d1179 Mon Oct 16 10:15:15 2017 -0700
    update human links.ra to use new URL for MGI
• src/hg/hgTracks/multiWig.c
  • lines changed 2, context: html, text, full: html, text
    89a26e18a779d448fb36d10c13f763030e8733cf Wed Oct 18 09:24:40 2017 -0700
    back out brain-dead change that breaks overlay "none" in multiwigs
• src/hg/hgc/gencodeClick.c
  • lines changed 11, context: html, text, full: html, text
    3aa01f2c24c384bcaeff2ca510be28c8afd2549f Mon Oct 23 09:06:02 2017 -0700
    added gencode version to all gencode hgc title
• src/hg/hgc/hgc.c
  • lines changed 22, context: html, text, full: html, text
    e73145dcb7ee87d0423dd3d19dd93fb42597920a Mon Oct 16 17:04:53 2017 -0700
    Removing further broken gad links in hgc. refs #20317
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 10, context: html, text, full: html, text
    01de096582c03a278ce69de1e9bea25ddb927d4d Fri Oct 20 14:30:19 2017 -0700
    Adding more required type= in custom track and also clarifying about group in assembly hubs vs. hubs/custom tracks refs #20354
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    a7b8720a72c79b3599ed58d8d347ea9edba45fac Thu Oct 19 08:35:56 2017 -0700
    Fixing typo from code review, refs #20346
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 58, context: html, text, full: html, text
    aa946e7eca1fb1c3c6a4bf39aeb1ffa0cbdace9f Wed Oct 18 16:50:26 2017 -0700
    Announcing GTEx eQTL tracks, refs #20236 and refs #15645
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 15, context: html, text, full: html, text
    2f69cb9edcc3cd09c481265ad06a36d5f0c1acdb Wed Oct 18 13:50:05 2017 -0700
    Adding Kate GTEx pub, not sure if it qualifies for Progress Report
  • lines changed 1, context: html, text, full: html, text
    78c12b10abdad6b271902793bbc3aef39a4f8fa7 Wed Oct 18 13:53:04 2017 -0700
    Removing extra period on pubs.html
  • lines changed 37, context: html, text, full: html, text
    eb7fe6ad6e1590204ac611105b6ce1f61d4f7522 Wed Oct 18 14:32:46 2017 -0700
    Moving 2017 pubs into A to Z order
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 2, context: html, text, full: html, text
    81842c2165adae48ce9f3d56c5838f78f32d3168 Mon Oct 16 15:08:20 2017 -0700
    expand nodes when something is dropped on them. Fix mouseover for "GO" button. Don't show scroll bars unless necessary
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    aa946e7eca1fb1c3c6a4bf39aeb1ffa0cbdace9f Wed Oct 18 16:50:26 2017 -0700
    Announcing GTEx eQTL tracks, refs #20236 and refs #15645
• src/hg/js/hgCollection.js
  • lines changed 6, context: html, text, full: html, text
    81842c2165adae48ce9f3d56c5838f78f32d3168 Mon Oct 16 15:08:20 2017 -0700
    expand nodes when something is dropped on them. Fix mouseover for "GO" button. Don't show scroll bars unless necessary
  • lines changed 2, context: html, text, full: html, text
    78b533e88567e07f40b41cb09ac848d10410c820 Mon Oct 16 17:23:16 2017 -0700
    open node instead of toggle when something is dropped on it.
  • lines changed 32, context: html, text, full: html, text
    7a6949d256eb4329de0a6cc7e0c2ae0da35b6bf0 Fri Oct 20 14:05:15 2017 -0700
    add + and - icons in front of tracks to make it easier to copy them into a collection or delete them from a collection
• src/hg/makeDb/doc/cebCap1/initialBuild.txt
  • lines changed 176, context: html, text, full: html, text
    68cdaf91b16a35decc8a9fe5bcfa4eae30f0b14d Thu Oct 19 13:17:44 2017 -0700
    done and marked QA Ready refs #20237
• src/hg/makeDb/doc/danRer11/initialBuild.txt
  • lines changed 343, context: html, text, full: html, text
    e45b293ff69b4cdbe89a3e9b778daa9a84228efd Fri Oct 20 15:08:02 2017 -0700
    updated ucscToRefSeq and chromAlias cpgIslands done refs #19459
• src/hg/makeDb/doc/hetGla1.txt
  • lines changed 76, context: html, text, full: html, text
    9f806b5451eb211049fd06458407641f12b81a03 Wed Oct 18 13:04:59 2017 -0700
    add ucscToINSDC and chromAlias tables refs #20304
• src/hg/makeDb/doc/hg38/multiz27way.txt
  • lines changed 1685, context: html, text, full: html, text
    49584f9001afc0b16257aa22e60be5236108aa1e Fri Oct 20 23:44:42 2017 -0700
    beginning to construct the 27-way refs #20216
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 80, context: html, text, full: html, text
    fe155fd1b7aff8f9a440e67651142e0a3c16b8f7 Wed Oct 18 10:17:40 2017 -0700
    ensGene v90 procedure refs #20304
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    bbc9ade0eb0b425ffeb8c211b50282fd83280c0d Thu Oct 19 15:51:09 2017 -0700
    Adding criGriChoV1 to beta genebank updates, refs#19228
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
  • lines changed 6, context: html, text, full: html, text
    e828765a12077044130f69a8d70e233188ebdbc9 Tue Oct 17 13:55:48 2017 -0700
    remove 2-way pseudo and ploy-A from HTML descriptions for lift of gencode to hg19
  • lines changed 20, context: html, text, full: html, text
    a7bbaef21490d4f4d24febc224b9e0b3f172bd3a Tue Oct 17 14:08:24 2017 -0700
    removed gencode exon support joiner rule for lifted releases
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    a7bbaef21490d4f4d24febc224b9e0b3f172bd3a Tue Oct 17 14:08:24 2017 -0700
    removed gencode exon support joiner rule for lifted releases
  • lines changed 11, context: html, text, full: html, text
    734617027bf534df651101cdde7091467644ba26 Wed Oct 18 10:19:55 2017 -0700
    adding neoSch1 rules refs #10883
  • lines changed 10, context: html, text, full: html, text
    0bb88ac4d891d682e7714b526c3878a03639832c Thu Oct 19 08:09:56 2017 -0700
    Added cebCap1 - White-faced sapajou/Cebus capucinus imitator refs #20237
  • lines changed 5, context: html, text, full: html, text
    5fb96f1f6b042377e1c0a01f9654faab443c7266 Thu Oct 19 17:11:06 2017 -0700
    cleaner tableCoverage for criGri1 and criGriChoV1 refs #19228
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5bab1cfa603dcece0510a42955d6f5db5ae2d4f0 Thu Oct 19 16:59:19 2017 -0700
    Quarantine chiGriChoV1 to dev and beta until rr release, refs #19228
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 4, context: html, text, full: html, text
    097c8b89621b6a2861229bd626b8a0b4a3840a5c Thu Oct 12 08:26:38 2017 -0700
    Fixing broken links found by the broken link report for canFam2, no Redmine.
• src/hg/makeDb/trackDb/dog/canFam2/uncertified.html
  • lines changed 1, context: html, text, full: html, text
    097c8b89621b6a2861229bd626b8a0b4a3840a5c Thu Oct 12 08:26:38 2017 -0700
    Fixing broken links found by the broken link report for canFam2, no Redmine.
• src/hg/makeDb/trackDb/drosophila/droAna2/gap.html
  • lines changed 4, context: html, text, full: html, text
    0046b8d7a1a1c4a2ff88863c4266b4c607f7ba11 Wed Oct 18 10:05:13 2017 -0700
    Fixing broken links found by the broken link report for droAna2, no Redmine.
• src/hg/makeDb/trackDb/drosophila/droAna2/gold.html
  • lines changed 4, context: html, text, full: html, text
    0046b8d7a1a1c4a2ff88863c4266b4c607f7ba11 Wed Oct 18 10:05:13 2017 -0700
    Fixing broken links found by the broken link report for droAna2, no Redmine.
• src/hg/makeDb/trackDb/drosophila/geneMapper.html
  • lines changed 1, context: html, text, full: html, text
    0046b8d7a1a1c4a2ff88863c4266b4c607f7ba11 Wed Oct 18 10:05:13 2017 -0700
    Fixing broken links found by the broken link report for droAna2, no Redmine.
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 16, context: html, text, full: html, text
    409fb2a686ae881443dbb72faa35826d4f965806 Thu Oct 19 10:35:10 2017 -0700
    correct overrides for danRer11 chainNet refs #19459
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.html
  • lines changed 9, context: html, text, full: html, text
    8643356a0dc39de9425b11b82d88adbcd5d2d46d Wed Oct 18 12:49:45 2017 -0700
    Update citation now that Nature manuscript has been published. refs #15646
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.v1.ra
  • lines changed 2, context: html, text, full: html, text
    8643356a0dc39de9425b11b82d88adbcd5d2d46d Wed Oct 18 12:49:45 2017 -0700
    Update citation now that Nature manuscript has been published. refs #15646
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cd7d3bd64131b2f114661a45c7e956e4884973cc Tue Oct 17 14:50:31 2017 -0700
    releasing GTEx eQTL, refs #20236
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 103, context: html, text, full: html, text
    1c0aaa4222e3494ae2c0e52219a91f4e5e7eaaaa Tue Oct 17 16:17:50 2017 -0700
    updated GENCODE credits and use general credits include HTML in super track descriptions
  • lines changed 5, context: html, text, full: html, text
    a4700079d60d9e3d0c45b5093fd2f6d5922ca7a2 Wed Oct 18 15:34:54 2017 -0700
    Small short label change and removing mention of v27lift37 release from html, refs #20145
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.html
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    e828765a12077044130f69a8d70e233188ebdbc9 Tue Oct 17 13:55:48 2017 -0700
    remove 2-way pseudo and ploy-A from HTML descriptions for lift of gencode to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.ra
  • lines changed 1, context: html, text, full: html, text
    030f4b22a035f0173b0ccfa2b4e35e9d0d98475b Wed Oct 18 14:45:18 2017 -0700
    Setting gencode v27 lift 37 track to hide by default, refs #20145
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    a4700079d60d9e3d0c45b5093fd2f6d5922ca7a2 Wed Oct 18 15:34:54 2017 -0700
    Small short label change and removing mention of v27lift37 release from html, refs #20145
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    3324f081c3a4b0f19cd0c19173e071406d6cac8b Wed Oct 18 15:50:12 2017 -0700
    Another small label change for v27 lift37, refs #20145
• src/hg/makeDb/trackDb/human/hg38/cancerExpr.ra
  • lines changed 1, context: html, text, full: html, text
    31e4f1a7c833fb9b423e938d4fa71729c1c2d964 Fri Oct 20 12:02:41 2017 -0700
    Adding the missing shared html page to the super track. Removing   HTML code for the barchart image. refs #19155
• src/hg/makeDb/trackDb/human/hg38/tcgaExpr.html
  • lines changed 1, context: html, text, full: html, text
    31e4f1a7c833fb9b423e938d4fa71729c1c2d964 Fri Oct 20 12:02:41 2017 -0700
    Adding the missing shared html page to the super track. Removing   HTML code for the barchart image. refs #19155
• src/hg/makeDb/trackDb/human/hg38/tcgaGeneExpr.html
  • lines changed 87, context: html, text, full: html, text
    53caae44d7049cebdee27a41e23e3b8126d72840 Fri Oct 20 12:17:25 2017 -0700
    Removing these two HTML pages since they are no longer used. They have been replaced with tcgaExpr.html, refs #19155
• src/hg/makeDb/trackDb/human/hg38/tcgaTranscExpr.html
  • lines changed 85, context: html, text, full: html, text
    53caae44d7049cebdee27a41e23e3b8126d72840 Fri Oct 20 12:17:25 2017 -0700
    Removing these two HTML pages since they are no longer used. They have been replaced with tcgaExpr.html, refs #19155
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 122, context: html, text, full: html, text
    1c0aaa4222e3494ae2c0e52219a91f4e5e7eaaaa Tue Oct 17 16:17:50 2017 -0700
    updated GENCODE credits and use general credits include HTML in super track descriptions
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    409fb2a686ae881443dbb72faa35826d4f965806 Thu Oct 19 10:35:10 2017 -0700
    correct overrides for danRer11 chainNet refs #19459
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    3187ea3d609ee0e9e356cf03f8979ad5df47b67a Fri Oct 20 16:51:19 2017 -0700
    Replacing 'human' with '$ organism' in the shared NCBI RefSeq HTML page, refs #18997
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 1, context: html, text, full: html, text
    2b7f27dd7b3db07fba4837694b5bedad155a96c0 Fri Oct 20 16:59:02 2017 -0700
    Adding a bigDataUrl trackDb setting to remove the MySQL dependency, refs #18897
• src/hg/makeDb/trackDb/snp131.html
  • lines changed 4, context: html, text, full: html, text
    097c8b89621b6a2861229bd626b8a0b4a3840a5c Thu Oct 12 08:26:38 2017 -0700
    Fixing broken links found by the broken link report for canFam2, no Redmine.
• src/hg/makeDb/trackDb/tagTypes.tab
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    5e876538e16ae8b15c9312e143f89c9923a772ef Thu Oct 19 17:15:14 2017 -0700
    forgot to add tagTypes.tab, per email from hiram and cath, no redmine
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    8d273b39a68e206a39aab59877a04f61dcd8f281 Wed Oct 18 18:25:29 2017 -0700
    catch up new chainNet tracks aotNan1 cebCap1 cerAty1 eulFla1 eulMac1 manLeu1 papAnu3 proCoq1 refs #20216
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 55, context: html, text, full: html, text
    78aa66b91a6609a2973748de7456dbb00d1b3b1f Thu Oct 19 10:29:43 2017 -0700
    adding danRer11 definition refs #19459
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
  • lines changed 17, context: html, text, full: html, text
    c2b8910c16c3b367357466c35e77faaf5b5cfc08 Thu Oct 19 15:43:45 2017 -0700
    adding target=_blank to clinvar outlinks, email from angie, no redmine
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
  • lines changed 13, context: html, text, full: html, text
    1c0aaa4222e3494ae2c0e52219a91f4e5e7eaaaa Tue Oct 17 16:17:50 2017 -0700
    updated GENCODE credits and use general credits include HTML in super track descriptions
• src/hg/makeDb/trackDb/wgEncodeGencodeDisplayLift1.shared.html
  • lines changed 214, context: html, text, full: html, text
    e828765a12077044130f69a8d70e233188ebdbc9 Tue Oct 17 13:55:48 2017 -0700
    remove 2-way pseudo and ploy-A from HTML descriptions for lift of gencode to hg19
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • lines changed 5, context: html, text, full: html, text
    097c8b89621b6a2861229bd626b8a0b4a3840a5c Thu Oct 12 08:26:38 2017 -0700
    Fixing broken links found by the broken link report for canFam2, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer11/description.html
  • lines changed 2, context: html, text, full: html, text
    26a23f1bbc7c533ad38f8991fea1b9d767b05b46 Fri Oct 20 13:56:54 2017 -0700
    Adding link to ncbi assembly page, refs #19459
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    e621cfb0f90e066337f1106c3e19eef2e2d58946 Fri Oct 20 14:10:15 2017 -0700
    add search rule for gold/assembly track refs #19459
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    db259d82f077f6d181572e6214596b449695413a Fri Oct 20 15:09:10 2017 -0700
    Making the default danRer11 more interesting hopefully, refs #19459
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    29593c5117f7e86293e259e17c058d66f7f63952 Fri Oct 20 15:10:34 2017 -0700
    Fixing merge conflict
• src/hg/utils/makefile
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    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 19, context: html, text, full: html, text
    c2b8910c16c3b367357466c35e77faaf5b5cfc08 Thu Oct 19 15:43:45 2017 -0700
    adding target=_blank to clinvar outlinks, email from angie, no redmine
• src/hg/utils/phyloTrees/218.nh
  • lines changed 218, context: html, text, full: html, text
    b9480d9a57979e46f2c799ae64d9c92fcee10c9d Thu Oct 19 13:13:55 2017 -0700
    adding all the primates refs #20216
• src/hg/utils/phyloTrees/218way.nh
  • lines changed 218, context: html, text, full: html, text
    3aaa735fbb09c303fc0817b87fee7e1ace15328d Thu Oct 19 13:23:43 2017 -0700
    correct name 218way refs #20216
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 35, context: html, text, full: html, text
    f9454407d04cdf29778cdadfadb1934864dbf134 Thu Oct 19 11:30:39 2017 -0700
    catching up with latest primate browsers refs #20216
• src/hg/utils/pslRc/makefile
  • lines changed 3, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/pslRc/pslRc.c
  • lines changed 55, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/pslRc/tests/expected/mrnaTest.psl
  • lines changed 7, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/pslRc/tests/expected/transTest.psl
  • lines changed 12, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/pslRc/tests/expected/withSeqTest.psl
  • lines changed 2, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/pslRc/tests/makefile
  • lines changed 35, context: html, text, full: html, text
    f7522e86274cd85385dd457579ee209867a9233d Mon Oct 16 15:04:57 2017 -0700
    added pslRc command
• src/hg/utils/vai.pl
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    9c97053863a72bc89330747d32a1c36d0bdfb706 Fri Oct 20 15:12:53 2017 -0700
    Adding HGVS options to vai.pl (HGVS terms are included by default if RefSeq transcripts are chosen).
• src/htslib/hts.c
  • lines changed 1, context: html, text, full: html, text
    208da7ba73e4a9a84a6427b41f8f456ae280ae9f Tue Oct 17 17:56:51 2017 -0700
    Fixing compile errors.
• src/htslib/sam.c
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    f63458a827952f14b1b1465a6da88c19d4facb9b Mon Oct 16 15:20:32 2017 -0700
    fixed compile error when CRAM enabled
• src/product/installer/browserSetup.sh
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    46d90a1ac820195a1ebae1afd7ac6949245feca7 Tue Oct 17 10:20:23 2017 -0700
    Modifying gbic to pull from genome-euro mysql server instead of ucsc if mirror is closer to europe, refs #20353
• src/utils/qa/runBits
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    4917a38c21a998a5f9710bb99b6d6e53f354c722 Thu Oct 19 12:03:21 2017 -0700
    Only check overlap with the gap table if we are not checking the gap table. Only check unbridged gaps if explicitly asked
  • lines changed 1, context: html, text, full: html, text
    bf6bfb867e296f780ca706f1203ae6d643cc5d52 Thu Oct 19 12:30:05 2017 -0700
    woops still want to check overlaps unless gap table
• src/utils/qa/weeklybld/buildEnv.csh
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    d640139afb9521940979e1c1ea473b8b0ed97e06 Mon Oct 23 09:54:49 2017 -0700
    v357 preview2 refs #20358
• src/utils/uniprotToTab
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    fe2357d86f58b3f8bc2855a0283ecb0bc455ae0c Thu Oct 19 15:49:30 2017 -0700
    changing comment in uniprot converter, email from Angie, no redmine

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