Commits for kate

v411_base to v412_preview (2021-03-01 to 2021-03-08) v412

c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700

• Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
  • src/hg/hgTracks/extTools.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 34, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 3, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/covidHgeMuts.html - lines changed 7, context: html, text, full: html, text

d04f55a6ff0fd8cbead80ada3a91dc9c5726cc93 Thu Oct 22 15:05:41 2020 -0700

• Add template for table of gene regions with data. refs #26351
  • src/hg/makeDb/trackDb/human/covidHgeMuts.html - lines changed 7, context: html, text, full: html, text

9e9fdcd37b60aa4186eeea2b2c61df277dbfeb5a Thu Oct 22 15:48:16 2020 -0700

• Add multi-region button to position line and lighten highlights on alternating regions. Part of improving multi-region features for sparse track use. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

2891e840cce943683ee4d828f1ee0c3787d7dd25 Mon Dec 28 10:36:10 2020 -0800

• Resolving merge conflict

425201196cb484fc22f36b66dcd15f370de800c8 Mon Dec 28 10:52:54 2020 -0800

• Better var name, slight color tweak on multi-region alt coloring change (for better visibility). refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

20e53653f690a97ca8b790b048629ea848d42144 Mon Dec 28 11:56:52 2020 -0800

• Resolving merge conflict

a0a09fc6e6c25f19d12fec548b834b931976207d Mon Dec 28 12:27:56 2020 -0800

• Minor cleanup. refs #26385
  • src/hg/hgTracks/extTools.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 2, context: html, text, full: html, text

7aa4e34c4a9855457ff806186ba65594e03ae6ac Wed Dec 30 16:03:35 2020 -0800

• First cut support for multiRegionBedUrl setting. refs #26385
  • src/hg/inc/hui.h - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 144, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

1e40d777521dac1839526c211b6c68fc0479f2db Mon Jan 4 10:07:19 2021 -0800

• Merge branch 'master' into multiRegionBedUrl
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

0c511f781581025b2963c78ef87f090435fa2a73 Mon Jan 4 16:13:07 2021 -0800

• Create trashfile for custom bed url, as multi-region code doesn't currently handle custom bed file (maybe change this later). refs #26385
  • src/hg/lib/hui.c - lines changed 53, context: html, text, full: html, text

d772009c6a70cb89a5baa33bc58499f1286827cb Fri Jan 8 09:21:34 2021 -0800

• Add padding to multi-region view and custom track generated by multiRegionBedUrl setting. refs #26385
  • src/hg/lib/hui.c - lines changed 8, context: html, text, full: html, text

953048f3d1eec8be6c580864e143c260ebb99aae Fri Jan 8 09:24:45 2021 -0800

• Merge branch 'master' into multiNoVirt

b4ed40256a8920e22356e9a810a699ee9b18de96 Fri Jan 8 09:25:01 2021 -0800

• Merge branch 'master' into multiButtonAndHlites

79e1e2ad3d1c2912d3de6700e644217fb4253e75 Fri Jan 8 09:27:38 2021 -0800

• Merge branch 'multiButtonAndHlites' into multiRegionBedUrl-ButtonAndHlites

87b7884a455030761304f18056a4e8a265b8cfaa Fri Jan 8 09:35:47 2021 -0800

• Resolving merge conflict
  • src/hg/hgTracks/hgTracks.c - lines changed 25, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 4, context: html, text, full: html, text

dcb87cc5b6d91351982761d957b1564b005acf9b Fri Jan 8 14:47:16 2021 -0800

• Fix merge problem
  • src/hg/hgTracks/hgTracks.c - lines changed 11, context: html, text, full: html, text

981add832de5beb7820a5337a4958f77d66aaad2 Fri Jan 8 14:48:43 2021 -0800

• Fix whitespace
  • src/hg/hgTracks/hgTracks.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

ce9ee89dedaffcf2eabf5fc68345b9c45469048b Wed Feb 24 16:15:41 2021 -0800

• Merge conflict
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 3, context: html, text, full: html, text

bd998f55bff39941de393c98ae3bb5e26ebdd836 Wed Feb 24 16:45:44 2021 -0800

• Changes to link wording, from review input. refs #26385
  • src/hg/lib/hui.c - lines changed 10, context: html, text, full: html, text

0ba941dfe2f00a5f8e62a44264489fd9253e504d Thu Feb 25 16:20:53 2021 -0800

• Fix missed virt->multi changes. TODO: #define.
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.c - lines changed 1, context: html, text, full: html, text

f53faebbe7aeb41c71623aeaea19cac84fb728af Thu Feb 25 16:47:50 2021 -0800

• Remove now-redundant multi-region button. Change exit button to be more informative. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 11, context: html, text, full: html, text

46826baa5de8a1d78807bdadf03881ec44f99c87 Tue Mar 2 16:17:02 2021 -0800

• Update make doc. refs #26876
  • src/hg/makeDb/doc/wuhCor1/variantMuts.txt - lines changed 2, context: html, text, full: html, text

6100258ab1f800bcaa254725037932027570f635 Tue Mar 2 16:19:36 2021 -0800

• Update make doc. refs #26876
  • src/hg/makeDb/doc/wuhCor1/variantMuts.txt - lines changed 2, context: html, text, full: html, text

d6e12e6e9c7dc09ef516984f150664165a48d9df Tue Mar 2 16:54:21 2021 -0800

• Tweak MR exit button label and mouseover. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 6, context: html, text, full: html, text

6da74d6034610d2ce3fe7ac708110c0e0e3d3a1c Tue Mar 2 17:02:43 2021 -0800

• Define string literal for multi-region chrom name. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.c - lines changed 1, context: html, text, full: html, text

fdef6066ef730b4a200e21e5c7b83c1be0804ee1 Tue Mar 2 17:03:10 2021 -0800

• Merge branch 'multiRegionBedUrl-All'

151e2e73ecaeca3adbd5088210d1c1c6683cb56c Tue Mar 2 17:09:00 2021 -0800

• Add new setting to enable link for multi-region display of regions of interest. refs #26385
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text

acf6e4da6ca00f6425abc54c690a97874234c30b Tue Mar 2 18:06:27 2021 -0800

• Add doc for multiRegionBedUrl setting. refs #26385
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 34, context: html, text, full: html, text

c9c3b2b4a6fb478e5cd4c8b987af8647e1ed5ee6 Wed Mar 3 09:51:12 2021 -0800

• Tweak link wording. refs #26385
  • src/hg/lib/hui.c - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text

b57070bef85b2c81db85b865075f2dfd3822b021 Wed Mar 3 09:58:45 2021 -0800

• Trivial text change. refs #26385
  • src/hg/lib/hui.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

3acf3830a00e2e600b62a41a4c4d56a6c2ef4a23 Wed Mar 3 10:12:36 2021 -0800

• Add link to COVID landing page to virus browser footer. refs #27117
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text

8b044d5f4044e8450db06f21481249e95bec7f85 Wed Mar 3 17:07:11 2021 -0800

• Multi-region link on hgTrackUi now turns track on in dense if it was hidden. Responding to QA note 22. refs #26385
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 10, context: html, text, full: html, text

35b3c483895c5ee49ad380200a342db959da6d3f Thu Mar 4 17:07:25 2021 -0800

• Add multi-region mode and improve layout a bit on position box popup. refs #26385
  • src/hg/hgTracks/config.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 24, context: html, text, full: html, text

23cc4593ea500af7329317e9ce60875dd458233a Fri Mar 5 12:12:51 2021 -0800

• Rejecting idea of MR exit button here. Removing useless OK button. refs #26385
  • src/hg/js/hgTracks.js - lines changed 9, context: html, text, full: html, text

feb9c1d10f245bbca5570655066783729acec65d Fri Mar 5 12:13:31 2021 -0800

• Merge branch 'multiRegion-PositionInfo'

a8be2f912e75d724a5d0d313e8488e82fd28e4ec Fri Mar 5 12:32:20 2021 -0800

• Retire 'exit multi-region' button idea. With multi-region button on position line and more informative mouseovers and popups it should be easier now for new multi-region users to exit. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 20, context: html, text, full: html, text

a8f242d425795e25ce0e0cce6d7cec9d8d8a3b6a Fri Mar 5 12:43:40 2021 -0800

• Context sensitive mouseover for multi-region button. refs #26385
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text

b84c039e779dc79ed16f6828cc17f30a7fae88a1 Fri Mar 5 12:53:24 2021 -0800

• Tweak wording on position info popup. refs #26385
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text