All File Changes

v358_base to v359_preview (2017-11-27 to 2017-12-04) v359

• src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
  • lines changed 6, context: html, text, full: html, text
    c8e7b00d1b147dafe2ee8f195eb7b855649991db Wed Nov 29 14:47:55 2017 -0800
    Adding symlinking after copying for consistency between cdwAddAssembly, cdwAddQaEnrichTarget, and other cdw utilities like cdwSubmit.
• src/hg/cirm/cdw/cdwFindSymlinkable/cdwFindSymlinkable.c
  • lines changed 1, context: html, text, full: html, text
    d8bb77800b2b6d58037b5947b1b2f08b617e3478 Tue Nov 28 19:48:05 2017 -0800
    minor wording improvement to message in cdwFindSymlinkable
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 31, context: html, text, full: html, text
    07b8577f0398e2db7a713a643e454a5ace7f663f Wed Nov 29 15:27:47 2017 -0800
    Making cdwMakeFileTags create a cdwFileFacets table that just has the cdwFileTags fields we are faceting on as an optimization.
• src/hg/cirm/cdw/cdwRunOnIds/cdwRunOnIds.c
  • lines changed 22, context: html, text, full: html, text
    e75c1e38cc92da2889a38381e89a8bf1dffc39af Thu Nov 9 15:33:40 2017 -0800
    Adding -dry and -one option, and restoring function from fail on sqlSafef.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 152, context: html, text, full: html, text
    896b704df6754e547327632c9f4f0a28f89b991f Wed Nov 29 15:32:34 2017 -0800
    Speeding up home page by using new facetFields routines to fetch data for the pie charts and the summary tags table mainly. This saved about 6 seconds. Also saved 1 second by reworking the query to find total bytes in files without a join. Also saved a second by just cutting the count of files you have access to.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    42c1bd36a61eb715b08d4e2cf45546c8a6ee5724 Wed Nov 29 15:34:23 2017 -0800
    Removing cdwLicensePlatePrefix function prototype since the actual function doesn't exist. Instead there is a function that does exist and was already in there that does the same thing. cdwLicensePlateHead.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 105, context: html, text, full: html, text
    c8e7b00d1b147dafe2ee8f195eb7b855649991db Wed Nov 29 14:47:55 2017 -0800
    Adding symlinking after copying for consistency between cdwAddAssembly, cdwAddQaEnrichTarget, and other cdw utilities like cdwSubmit.
• src/hg/hgTables/longRange.c
  • lines changed 2, context: html, text, full: html, text
    bf536f84ca4ea0d5ff0578b03d04644585647e25 Mon Nov 27 15:28:31 2017 -0800
    Suppress 'view schema' links for longTabix until view is implemented. refs #20599
• src/hg/hgTracks/longRangeTrack.c
  • lines changed 4, context: html, text, full: html, text
    364d1d51ed66e45f7db0cca796863bbdf438b6ce Tue Nov 28 13:05:53 2017 -0800
    Add maxHeightPixels setting support to longTabix track type. refs #17512
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    248dc7d37c584962501b4a765d5c0119724e8710 Tue Nov 28 11:29:30 2017 -0800
    Have longTabix use UDC for efficiency (as done with bedTabix). refs #20599
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 12, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
  • lines changed 4, context: html, text, full: html, text
    3d845588d110ade10dbed07299f81e6495b7679b Wed Nov 29 11:06:42 2017 -0800
    some cleanup of bigNarrowPeak doc
• src/hg/htdocs/cite.html
  • lines changed 1, context: html, text, full: html, text
    a30afbe845aa91df3c8cb95e7420ae50e0fd76c7 Tue Nov 28 18:12:03 2017 -0800
    Fixing minor typo, no RM
• src/hg/htdocs/goldenPath/help/bigNarrowPeak.html
  • lines changed 77, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 11, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 1, context: html, text, full: html, text
    33bd1837b2e0e7b7651c53bdf6e05eabcc74bdc8 Tue Nov 28 16:44:47 2017 -0800
    Fixing minor typo, no RM
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 26, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
  • lines changed 3, context: html, text, full: html, text
    3d845588d110ade10dbed07299f81e6495b7679b Wed Nov 29 11:06:42 2017 -0800
    some cleanup of bigNarrowPeak doc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 24, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
  • lines changed 4, context: html, text, full: html, text
    3d845588d110ade10dbed07299f81e6495b7679b Wed Nov 29 11:06:42 2017 -0800
    some cleanup of bigNarrowPeak doc
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    a72c29b4506e4a5fb3a8287412ff17e489a399e0 Mon Nov 27 12:44:30 2017 -0800
    Updating the publication date to match the date on the linked report, no Redmine.
• src/hg/htdocs/images/phylo/xenTro9_11way.png
  • lines changed 0, context: html, text, full: html, text
    5c33cf3db46230f0c83f000ee031ff0f34ea51b3 Wed Nov 29 17:29:11 2017 -0800
    phylo image for xenTro9 11-way alignment refs #19151
• src/hg/inc/facetField.h
  • lines changed 31, context: html, text, full: html, text
    c6be16ecff0742cd0612109048f6d7723f797025 Thu Nov 30 16:04:38 2017 -0800
    Oops, forgot to add this with the corresponding .c file.
• src/hg/inc/longRange.h
  • lines changed 3, context: html, text, full: html, text
    364d1d51ed66e45f7db0cca796863bbdf438b6ce Tue Nov 28 13:05:53 2017 -0800
    Add maxHeightPixels setting support to longTabix track type. refs #17512
• src/hg/js/hgTracks.js
  • lines changed 21, context: html, text, full: html, text
    177fd93a7c0b621578f7606df0b49c10bb47eda4 Wed Nov 29 15:08:45 2017 -0800
    remove add to collection right-click menus from hgTracks
• src/hg/lib/bigNarrowPeak.as
  • lines changed 14, context: html, text, full: html, text
    59c8b7dc00d4acb5654d66cdae5cc97881f33f67 Tue Nov 28 15:41:23 2017 -0800
    bigNarrowPeak doc
• src/hg/lib/facetField.c
  • lines changed 147, context: html, text, full: html, text
    92b0b750862917e18784fcf1bb77c3f383b31ade Mon Nov 27 12:56:48 2017 -0800
    Adding count to label for other.
• src/hg/lib/hAnno.c
  • lines changed 2, context: html, text, full: html, text
    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    a2dbf4340f99161cce599508bb219b7fcacab764 Mon Nov 27 14:52:41 2017 -0800
    make sure button id's are all unique in compositieUi without composites. #20581
  • lines changed 6, context: html, text, full: html, text
    bf536f84ca4ea0d5ff0578b03d04644585647e25 Mon Nov 27 15:28:31 2017 -0800
    Suppress 'view schema' links for longTabix until view is implemented. refs #20599
• src/hg/lib/longRange.c
  • lines changed 8, context: html, text, full: html, text
    364d1d51ed66e45f7db0cca796863bbdf438b6ce Tue Nov 28 13:05:53 2017 -0800
    Add maxHeightPixels setting support to longTabix track type. refs #17512
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    8d3e14df49bba90d2514f1ead65d8f94e1d05781 Wed Nov 29 15:34:50 2017 -0800
    Adding facetField.c to the build.
• src/hg/lib/refSeqFuncElems.as
  • lines changed 6, context: html, text, full: html, text
    3ab97c0ed056b21d4c061f9cb0055f30391758ee Wed Nov 29 14:07:07 2017 -0800
    Updated refSeqFuncElems track to use NCBI's coloring and labeling scheme; also scrape PMIDs from note and function attributes. refs #19638
  • lines changed 1, context: html, text, full: html, text
    e41e01c3bbfda0c94e7a3b9509463bae02500a4a Wed Nov 29 14:35:01 2017 -0800
    Clarification for geneIds column description.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    145c153ea864c5f71b570be35c9b619b0b174bcd Wed Nov 29 17:22:50 2017 -0800
    turn note into comment refs #20590
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 41, context: html, text, full: html, text
    3ab97c0ed056b21d4c061f9cb0055f30391758ee Wed Nov 29 14:07:07 2017 -0800
    Updated refSeqFuncElems track to use NCBI's coloring and labeling scheme; also scrape PMIDs from note and function attributes. refs #19638
• src/hg/makeDb/doc/mm10.txt
  • lines changed 39, context: html, text, full: html, text
    3ec2248dca789bbbc6b602168c507263a141a0ef Wed Nov 29 14:33:43 2017 -0800
    Updated mm10 refSeqFuncElems track. refs #19638
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    9d519d19d37dfca9ce367226391f31055ba8e79d Mon Dec 4 08:00:46 2017 -0800
    Turning on hgwbeta genbank updates for xenTro9
• src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    6b4f44dbcad801804f6ce8e598297ef83cdc2c68 Thu Nov 30 15:30:25 2017 -0800
    Fixing matrix and chain lines for the chain/net tracks, refs #16036
• src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    6b4f44dbcad801804f6ce8e598297ef83cdc2c68 Thu Nov 30 15:30:25 2017 -0800
    Fixing matrix and chain lines for the chain/net tracks, refs #16036
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 2, context: html, text, full: html, text
    4534379d8f6c882f39a9c1bc00d0d0108443e127 Tue Nov 28 09:00:24 2017 -0800
    Fixing broken links for equCab2, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 2, context: html, text, full: html, text
    3b125ccfdba60c739ee65f7d0b4c1cffd7df4d5b Wed Nov 29 15:40:36 2017 -0800
    Testing the 'new' icon on beta, refs #20270
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 12, context: html, text, full: html, text
    d71db979f4f8cfd1e60ed93ee4ac6ae284334b74 Fri Dec 1 14:12:09 2017 -0800
    Adding hg38 30way download links to match other cons tracks, refs #20216
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    b34d31b784d95ee5db4af755eaebd7bd4a242ae7 Fri Dec 1 15:53:23 2017 -0800
    Switching to the newer table-border style, refs #20216
• src/hg/makeDb/trackDb/refGenePfam.html
  • lines changed 6, context: html, text, full: html, text
    c57637f8d88e8ce4bb802b67ef54739e4bb01788 Tue Nov 28 16:29:36 2017 -0800
    Updating pfam desc page for hg18,19,38,mm9,10,dm6, refs #18770
  • lines changed 13, context: html, text, full: html, text
    bfc2e59761a9eab06f0a13b815edb05254b74262 Fri Dec 1 12:23:10 2017 -0800
    Pfam pages, making HMMER bug note version agnostic and removing forum link, refs #20610
• src/hg/makeDb/trackDb/refSeqFuncElems.html
  • lines changed 14, context: html, text, full: html, text
    36ccf9dfc32490e099b5686c9a4823cb4d77b9cc Wed Nov 29 15:39:19 2017 -0800
    Added description of NCBI color scheme. refs #19638
• src/hg/makeDb/trackDb/template.html
  • lines changed 89, context: html, text, full: html, text
    d8d9a7a68d4ff5ed2ab861f0e4d51691b91422bb Wed Nov 29 16:18:20 2017 -0800
    adding a template track doc page, after discussion with brian lee
• src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
  • lines changed 8, context: html, text, full: html, text
    965b634753d83ac681ef41f0834513e3562b27b5 Mon Dec 4 09:48:03 2017 -0800
    Removing release tag to get xenTro9 and xenLae2 chainNets public, refs #19151
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    3ab97c0ed056b21d4c061f9cb0055f30391758ee Wed Nov 29 14:07:07 2017 -0800
    Updated refSeqFuncElems track to use NCBI's coloring and labeling scheme; also scrape PMIDs from note and function attributes. refs #19638
• src/hg/makeDb/trackDb/ucscGenePfam.html
  • lines changed 7, context: html, text, full: html, text
    c57637f8d88e8ce4bb802b67ef54739e4bb01788 Tue Nov 28 16:29:36 2017 -0800
    Updating pfam desc page for hg18,19,38,mm9,10,dm6, refs #18770
  • lines changed 13, context: html, text, full: html, text
    e00af9d8398edb546ac541b99815a6bc7e43a0ed Wed Nov 29 15:51:43 2017 -0800
    making some changes to pfam html page after discussion with braney, refs #20610
  • lines changed 11, context: html, text, full: html, text
    bfc2e59761a9eab06f0a13b815edb05254b74262 Fri Dec 1 12:23:10 2017 -0800
    Pfam pages, making HMMER bug note version agnostic and removing forum link, refs #20610
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 1, context: html, text, full: html, text
    373ffb47e28f5ff5972f261c900d7c99e1351924 Wed Nov 29 13:59:23 2017 -0800
    Informing users about preview browser link after comments in code review, refs #20585
  • lines changed 14, context: html, text, full: html, text
    13a6238eb94fa745e8f471d8211f0c0ee2281b7d Wed Nov 29 21:59:38 2017 -0800
    clean up 11-way description refs #19151
• src/hg/oneShot/freen/freen.c
  • lines changed 122, context: html, text, full: html, text
    c7686e10cf2c33c4008a2e1c1528f53fc9ff6c98 Wed Nov 29 15:35:12 2017 -0800
    Freen tests facetField.c
• src/hg/utils/automation/parseRefSeqFuncElems
  • lines changed 160, context: html, text, full: html, text
    3ab97c0ed056b21d4c061f9cb0055f30391758ee Wed Nov 29 14:07:07 2017 -0800
    Updated refSeqFuncElems track to use NCBI's coloring and labeling scheme; also scrape PMIDs from note and function attributes. refs #19638
  • lines changed 3, context: html, text, full: html, text
    03286893debda8e2edc28a7dde6302cf333ca465 Wed Nov 29 15:38:45 2017 -0800
    parseRefSeqFuncElems: sometimes there is no feat_class and no note for sequence features; use standard_name if present.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 9, context: html, text, full: html, text
    b75505e6b3a7c27ee7e2c9aa185216b65b6ee1c1 Mon Nov 27 15:29:05 2017 -0800
    Make hubCheck aware of type longTabix. refs #20599
• src/inc/annoStreamLongTabix.h
  • lines changed 11, context: html, text, full: html, text
    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/inc/annoStreamTabix.h
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    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/inc/bedTabix.h
  • lines changed 5, context: html, text, full: html, text
    e52349aa29cae89f4e9fd765da98d1a46ad2cbe9 Mon Nov 27 14:41:59 2017 -0800
    add header for bedTabix files
• src/inc/longTabix.h
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    de8ca293b4eda9ba40ff55ffb3bf94827a65b561 Mon Nov 27 15:42:22 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/lib/annoStreamLongTabix.c
  • lines changed 208, context: html, text, full: html, text
    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/lib/annoStreamTabix.c
  • lines changed 228, context: html, text, full: html, text
    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/lib/bedTabix.c
  • lines changed 6, context: html, text, full: html, text
    e52349aa29cae89f4e9fd765da98d1a46ad2cbe9 Mon Nov 27 14:41:59 2017 -0800
    add header for bedTabix files
• src/lib/longTabix.c
  • lines changed 44, context: html, text, full: html, text
    de8ca293b4eda9ba40ff55ffb3bf94827a65b561 Mon Nov 27 15:42:22 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/lib/makefile
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    3c9f824a9764c5eed782ae3f07146aadecec74f0 Mon Nov 27 15:07:15 2017 -0800
    Cleanup to ease some fixes to longTabix.
• src/utils/qa/weeklybld/buildEnv.csh
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    e303fb39c0c5434de89fa47d3359a98d2d08f081 Mon Dec 4 10:00:14 2017 -0800
    v359 preview1 refs #20479

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• files changed: 70