All File Changes

v341_preview2 to v341_base (2016-10-31 to 2016-11-07) v341

• src/browserbox/root/updateBrowser.sh
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    1ebe979040195c2060ca0c1332638dd254430892 Thu Nov 3 14:07:30 2016 -0700
    fixing 0-byte stuck html file in gbib update, refs #18337
• src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
  • lines changed 96, context: html, text, full: html, text
    fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
    Adding in the download meta data option to the analysis query tab, refs #17870
• src/hg/cirm/cdw/cdwGetMetadataAsFile/makefile
  • lines changed 16, context: html, text, full: html, text
    fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
    Adding in the download meta data option to the analysis query tab, refs #17870
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    ca112199cb040b7df91678144fb9ab6cc4290f77 Mon Oct 31 15:16:49 2016 -0700
    Expanding buffer for large tag values.
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    fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
    Adding in the download meta data option to the analysis query tab, refs #17870
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 122, context: html, text, full: html, text
    fde95b41e4ce0f67bc81151e71805a9a32d0d509 Fri Nov 4 10:21:54 2016 -0700
    Adding in the download meta data option to the analysis query tab, refs #17870
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 138, context: html, text, full: html, text
    a7255af50076812432601cb7d5f81dfd55d5ec05 Wed Nov 2 12:58:04 2016 -0700
    Updating the accepted tags to include the MISCE terms that Clay and JCVI have been working on, refs #17334
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    83ff9557037715521b9cb3714ec7989763b92aa7 Wed Nov 2 16:17:40 2016 -0700
    Updating cv checks for MISCE terms, and fixing a few typos in MISCE tags and removing old tag list and alphabetizing new tags list.
• src/hg/hgc/hgc.c
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    0684c7b8dc207944939299c15c37aa8356a90fbb Tue Nov 1 12:52:03 2016 -0700
    no Gene Tree link on non-coding genes refs #18240
• src/hg/hgc/vcfClick.c
  • lines changed 17, context: html, text, full: html, text
    90f7a592103554129bc969299a356439ae02336c Thu Nov 3 10:56:04 2016 -0700
    VCF details: don't show name if empty or placeholder. Show ExAC link before dbSNP link and make ExAC link label more consistent with ExAC display. refs #18284
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    8a0897c2c6eaa58fc358344d199b6b6d28da49c6 Fri Nov 4 09:33:46 2016 -0700
    adding . as a possible letter for strand to bed documentation, no refseq
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    a357ce2e9b407564bc35e54b0ea0b4c6d5e79848 Fri Nov 4 09:40:27 2016 -0700
    fixing bed docs some more, no redmine
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 16, context: html, text, full: html, text
    87cb00b115a19d5642c7e31db84644e75edbf18d Mon Oct 31 11:24:11 2016 -0700
    editing credits for panTro5 refs #17817
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    dd0a103495388a3b1b52d7dc61479165dea89ece Mon Oct 31 14:53:27 2016 -0700
    updating Credits.html for Chimp refs #17817
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 12, context: html, text, full: html, text
    a9776d812aca78c00e47a513f40d0b29a345f6f3 Wed Nov 2 09:42:52 2016 -0700
    added HGVS terms, refs #18079
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
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    bf33b30d0b9c6988a61ba72ba347ad20b1f90dbb Wed Nov 2 14:49:42 2016 -0700
    Changing readme
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 13, context: html, text, full: html, text
    799e5c2048fab6f0beaf9cb733c15cb4c98fee9b Wed Nov 2 14:13:43 2016 -0700
    Added an announcement about the new chromAlias table for hg38, refs #18250
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    9161c64d63829b54852ff00e9c700e3e3dd4d529 Wed Nov 2 14:30:25 2016 -0700
    Putting the correct date, refs#18250
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    344bd499b559359b38e0f8988ac9e20e2deff7c0 Thu Nov 3 09:49:45 2016 -0700
    Changing the date and formatting for the chromAlias announcement, ref #18250
• src/hg/htdocs/images/Drosophila_simulans.jpg
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    edba1b0991019bb90d73debfc028fcdc28f4e5b4 Tue Nov 1 14:06:34 2016 -0700
    for droSim2 browser wikimedia commons Dr Andrew Weeks https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg refs #18269
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    967b5384a5eca550af10177654cf924937dabf22 Wed Nov 2 14:25:18 2016 -0700
    Adding a short headline for the new chromAlias table, refs# 18250
  • lines changed 1, context: html, text, full: html, text
    9161c64d63829b54852ff00e9c700e3e3dd4d529 Wed Nov 2 14:30:25 2016 -0700
    Putting the correct date, refs#18250
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    8b71d6889ca58bfa8bff17469aeab3532befe245 Wed Nov 2 14:31:53 2016 -0700
    Forgot to change the link to the newsarch.html page, refs #18250
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    344bd499b559359b38e0f8988ac9e20e2deff7c0 Thu Nov 3 09:49:45 2016 -0700
    Changing the date and formatting for the chromAlias announcement, ref #18250
• src/hg/inc/versionInfo.h
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    a1494fec288ca82de0a42c1f6315412fba7a154a Mon Nov 7 10:06:28 2016 -0800
    New version number v341
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    8cc61900672e957331a5ae02cea5b7cc53f8e5f9 Mon Oct 31 14:32:12 2016 -0700
    check to see if tracks have duplicated names .
• src/hg/makeDb/crisprTrack/createBigBed.py
  • lines changed 2, context: html, text, full: html, text
    a46dc06c474d2bddcfe5743138e256ae35387459 Tue Nov 1 13:28:00 2016 -0700
    tiny change to crispr bigBed creator, refs #17235
• src/hg/makeDb/doc/dm3.txt
  • lines changed 69, context: html, text, full: html, text
    aa99224331a34949e02ff3cc8942da2fd161ef3b Wed Nov 2 10:59:38 2016 -0700
    liftOver to droSim2 per user request refs #18269
• src/hg/makeDb/doc/droSim1.txt
  • lines changed 15, context: html, text, full: html, text
    826af23bad85f06440c75d2f226160f0f21eaab2 Wed Nov 2 11:05:39 2016 -0700
    liftOver to droSim2 refs #18269
• src/hg/makeDb/doc/droSim2/initialBuild.txt
  • lines changed 564, context: html, text, full: html, text
    653888d85818c108e9505c4d0ec4f801c459128b Wed Nov 2 11:06:51 2016 -0700
    to construct dm3 to droSim2 liftOver refs #18269
• src/hg/makeDb/doc/mouseStrains/groups.txt
  • lines changed 39, context: html, text, full: html, text
    5c72520bca3d8ba7f0fe49ed1f1b8b473142a3ed Mon Nov 7 09:44:49 2016 -0800
    the groups.txt file for the mouse strains refs #13553
• src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt
  • lines changed 160, context: html, text, full: html, text
    82cec746b350c7a69784e7f66959b36351c2ce14 Mon Nov 7 09:36:27 2016 -0800
    the genomes.txt file refs #13553
  • lines changed 33, context: html, text, full: html, text
    43fd5b317fb16c32cf2895b70051c82fc4088e50 Mon Nov 7 09:53:41 2016 -0800
    adding blat servers refs #13553
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    a08ce839f61a97d23b493640d7510ad13341990f Mon Nov 7 09:54:38 2016 -0800
    adding blat servers refs #13553
• src/hg/makeDb/doc/mouseStrains/mouseStrainsBuildNotes.txt
  • lines changed 84, context: html, text, full: html, text
    47802304b1952dbda253f7b3c9d17cf0f8bf2d2e Sat Nov 5 14:14:30 2016 -0700
    adding build notes refs #13553
• src/hg/makeDb/doc/mouseStrains/rnaSeqStar.html
  • lines changed 190, context: html, text, full: html, text
    910034e3ec1547b950e6434a7a98486ddb4cb5d9 Tue Nov 1 11:21:52 2016 -0700
    description page for RNA Seq Star tracks, a copy of this file is in each species html directory refs #13553
• src/hg/makeDb/schema/all.joiner
  • lines changed 85, context: html, text, full: html, text
    dcd380328b878973aec7a29389391dbb03dd784c Tue Nov 1 16:56:47 2016 -0700
    added forgotten VM11 join check
• src/hg/makeDb/trackDb/drosophila/droSim2/description.html
  • lines changed 64, context: html, text, full: html, text
    a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
    adding droSim2 to the build refs #18269
• src/hg/makeDb/trackDb/drosophila/droSim2/gap.html
  • lines changed 29, context: html, text, full: html, text
    a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
    adding droSim2 to the build refs #18269
• src/hg/makeDb/trackDb/drosophila/droSim2/gold.html
  • lines changed 34, context: html, text, full: html, text
    a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
    adding droSim2 to the build refs #18269
• src/hg/makeDb/trackDb/drosophila/droSim2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
    adding droSim2 to the build refs #18269
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.ra
  • lines changed 1, context: html, text, full: html, text
    f7d15a2fd90040351e6b92c4e1dac320ac68e63b Tue Nov 1 15:29:40 2016 -0700
    updated hgFindSpec to match naming convention change on GENCODE 2-way pseudogene track
• src/hg/makeDb/trackDb/makefile
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    a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700
    adding droSim2 to the build refs #18269
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeCredits1.shared.html
  • lines changed 110, context: html, text, full: html, text
    7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
    updated GENCODE credits section
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    60a8742482f1c4cb169a020d4ff6980936e87e2c Wed Nov 2 08:34:54 2016 -0700
    Fixing broken td tag, removing extra comma, making APPRIS link open in new tab, and making APPRIS lines fit within our less 100 char limits, refs #18295
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeDisplay1.shared.html
  • lines changed 235, context: html, text, full: html, text
    7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
    updated GENCODE credits section
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    60a8742482f1c4cb169a020d4ff6980936e87e2c Wed Nov 2 08:34:54 2016 -0700
    Fixing broken td tag, removing extra comma, making APPRIS link open in new tab, and making APPRIS lines fit within our less 100 char limits, refs #18295
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
  • lines changed 122, context: html, text, full: html, text
    7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
    updated GENCODE credits section
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.html
  • lines changed 319, context: html, text, full: html, text
    7ba9ed84cc188859e75622549292ff3a5c7ff2bd Tue Nov 1 16:51:40 2016 -0700
    updated GENCODE credits section
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
  • lines changed 1, context: html, text, full: html, text
    f7d15a2fd90040351e6b92c4e1dac320ac68e63b Tue Nov 1 15:29:40 2016 -0700
    updated hgFindSpec to match naming convention change on GENCODE 2-way pseudogene track
• src/hg/pslCheck/pslCheck.c
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    f1ed9037745e40b85f0e3908f6e8f1aa497cf753 Sun Nov 6 16:09:27 2016 -0800
    added option to pslCheck to string qName uniqueness modifiers
• src/hg/utils/automation/extractSource.pl
  • lines changed 44, context: html, text, full: html, text
    bed79fc1964b5e7f176df34bbdf5d6675bc9a28b Tue Nov 1 10:49:34 2016 -0700
    to fixup extraction of source identity from Ensembl gtf file refs #18240
• src/inc/bamFile.h
  • lines changed 4, context: html, text, full: html, text
    6d90b13178a35682a27514cf704f7b05794e7192 Wed Nov 2 14:18:48 2016 -0700
    Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
• src/lib/bamFile.c
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    07f0e0134a6eee29337add57582421937c617e9a Wed Nov 2 14:17:47 2016 -0700
    Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
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    196d206a199ee47dc303b5ddf54170f89e4daa75 Thu Nov 3 17:13:25 2016 -0700
    correctly counting matches and mis matches refs #13673
• src/lib/htmlPage.c
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    596fceb9da320bd456bbd4cda8571d4a62cc329f Mon Oct 31 12:03:18 2016 -0700
    Relaxing some validations to accommodate newer web pages.
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    9562808bb257905689c06d196305e0b8234bf05b Mon Oct 31 12:14:08 2016 -0700
    Improving behavior when missing technically optional head section.
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    41f2f92517eff6f5b8477bdd90bfe33799eeedd0 Mon Oct 31 12:28:42 2016 -0700
    Adding DIV SCRIPT and SVG to tags checked for nesting.
• src/tagStorm/tagStormQuery/tagStormQuery.c
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    12c561f936552b6604e16e209cbff155516966ca Wed Nov 2 15:16:44 2016 -0700
    Fixed year old typo!
• src/utils/bamToFastq/bamToFastq.c
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    a14d8dea71b926b326385cdd03a50b5db372240c Wed Nov 2 14:22:24 2016 -0700
    Updating to use htslib.
• src/utils/bamToFastq/makefile
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    a14d8dea71b926b326385cdd03a50b5db372240c Wed Nov 2 14:22:24 2016 -0700
    Updating to use htslib.
• src/utils/bamToPsl/bamToPsl.c
  • lines changed 80, context: html, text, full: html, text
    3ad4f4c509134534060643ed1152f4629aab172e Wed Nov 2 14:15:58 2016 -0700
    First cut of a bamToPsl utility.
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    2bd5caf8ce518d13cefc69de0d084228cf7712fe Fri Nov 4 13:36:48 2016 -0700
    adding useful options refs #13673
• src/utils/bamToPsl/makefile
  • lines changed 4, context: html, text, full: html, text
    3ad4f4c509134534060643ed1152f4629aab172e Wed Nov 2 14:15:58 2016 -0700
    First cut of a bamToPsl utility.
• src/utils/doLocusName
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    a823a26a0ed014c44482f50eb1c4072b3860f9de Mon Oct 31 14:27:59 2016 -0700
    small fix to doLocusName to handle genes with with spaces in names
• src/utils/htmlCheck/htmlCheck.c
  • lines changed 9, context: html, text, full: html, text
    4d0515666d53ed314b503f52a80cfb5a3744af28 Mon Oct 31 12:54:32 2016 -0700
    Fixing so that you can run htmlCheck on local files rather than just URLS.
• src/utils/makefile
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    93115ea6e9d63814f717023f1e798d1025ad494c Fri Nov 4 13:37:30 2016 -0700
    adding bamToPsl to utils refs #13673
• src/utils/qa/weeklybld/buildEnv.csh
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    8b5a8239d2432475ec19002c09963f7d3956de03 Mon Nov 7 10:05:28 2016 -0800
    v341 final build refs #18302

• lines changed: 3317
• files changed: 68