All File Changes

v410_base to v411_preview (2021-02-08 to 2021-02-15) v411

• confs/preview.hg.conf
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    08c5559d1b35c794f1dad0ea81a3d2bd58d0b4cc Sun Feb 14 01:11:43 2021 -0800
    Installing updated hg.conf files from UCSC servers
• src/hca/hcaColorCells/hcaColorCells.c
  • lines changed 21, context: html, text, full: html, text
    396eb0a4fd1d3b5d41530a62a5d9719a21eace93 Mon Feb 1 09:29:26 2021 -0800
    Removed unused refCorrelate in response to code review #26824
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    aef030e99fe05f80367079483c7b15367d5b2b16 Mon Feb 1 09:34:09 2021 -0800
    Moving unpackHexString to library per code review #26824
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    01212f5c7964f242897e015217ba2a149f5c23bf Thu Jan 28 17:54:31 2021 -0800
    Reducing facet size to 15
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    f696e3739df240549d0ef2a172a13f7b4d2a8433 Thu Jan 28 21:26:51 2021 -0800
    Making facet_op be not hard coded
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    dacec81196967c10d494c7b77a49cc41a5aa63ce Thu Jan 28 22:10:56 2021 -0800
    Making a couple of more variables use the varPrefix rather than be hard coded.
  • lines changed 9, context: html, text, full: html, text
    19e6e03d64ce54f9db60a93734cd3b573eb0446b Fri Jan 29 09:07:37 2021 -0800
    I believe I got all the faceted variables using the varPrefix. Tested this by having two faceted tables on the same page and it worked. Looks clean by cartDump too.
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    f92a444ad6ba92b1190c76629b18d219e1809c7c Tue Feb 9 07:49:02 2021 -0800
    fixing a spurious linebreak in hgBlat that i introduced myself, refs #26918
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    2fa2ae0051bcf6ed6c3ca627ec5b700c828e9d04 Wed Feb 10 04:59:15 2021 -0800
    fixing links in new alt/fix notes in hgBlat, found by Gerardo, refs #26918
• src/hg/hgFacetedBars/hgFacetedBars.c
  • lines changed 120, context: html, text, full: html, text
    1aded0d32b0a11b176a69e55e718fc0a69cfc38c Thu Jan 28 08:30:15 2021 -0800
    Most if all of the buttons and links from the cirm faceted site are working. This is still very much just a prototype though.
  • lines changed 31, context: html, text, full: html, text
    078fcca1d679a770b100f71cfcd514b412f1e88d Thu Jan 28 17:50:06 2021 -0800
    Commenting and cleaning up code. Making it only show 10 things in a facet by default.
  • lines changed 4, context: html, text, full: html, text
    f696e3739df240549d0ef2a172a13f7b4d2a8433 Thu Jan 28 21:26:51 2021 -0800
    Making facet_op be not hard coded
  • lines changed 89, context: html, text, full: html, text
    dacec81196967c10d494c7b77a49cc41a5aa63ce Thu Jan 28 22:10:56 2021 -0800
    Making a couple of more variables use the varPrefix rather than be hard coded.
  • lines changed 68, context: html, text, full: html, text
    19e6e03d64ce54f9db60a93734cd3b573eb0446b Fri Jan 29 09:07:37 2021 -0800
    I believe I got all the faceted variables using the varPrefix. Tested this by having two faceted tables on the same page and it worked. Looks clean by cartDump too.
  • lines changed 38, context: html, text, full: html, text
    e46b8109fd1277a3abbda51a7da0434863eabc77 Fri Jan 29 16:10:27 2021 -0800
    Removed second table that was there just for testing. Transitioning away from table for metadata to tab-sep-file.
  • lines changed 111, context: html, text, full: html, text
    51609277effd21687e81efe1d1e2c58ef21328e8 Sat Jan 30 09:06:31 2021 -0800
    Got this to work with the table in a tsv file and with graphical bars as part of the table. I'm stopping development on this piece since I think I can integrate it into hgc (in fact I have) and into hgTrackUi rather than needing a separate CGI. Still a lot of refactoring to do. I'll probably be moving this module into oneShot soon. No need to review. It has served it's purpose, and the code here will be redistributed and libified.
  • lines changed 181, context: html, text, full: html, text
    a79fba9b734cc2dc74f8fe6365fe833f7a14c06b Mon Feb 1 17:27:55 2021 -0800
    Adjusting to use the new interface to facetedTable, which now resides in a library module. No need to review. This module is about to get moved to oneShot.
  • lines changed 166, context: html, text, full: html, text
    2f6acb208e6abe1f09be24d4a6bec948148a5ee9 Mon Feb 1 17:29:10 2021 -0800
    Moving this to directory for exploratory non-reviewed code. It was a nice little platform to work out ideas.
• src/hg/hgFacetedBars/makefile
  • lines changed 18, context: html, text, full: html, text
    1aded0d32b0a11b176a69e55e718fc0a69cfc38c Thu Jan 28 08:30:15 2021 -0800
    Most if all of the buttons and links from the cirm faceted site are working. This is still very much just a prototype though.
  • lines changed 18, context: html, text, full: html, text
    2f6acb208e6abe1f09be24d4a6bec948148a5ee9 Mon Feb 1 17:29:10 2021 -0800
    Moving this to directory for exploratory non-reviewed code. It was a nice little platform to work out ideas.
• src/hg/hgGene/hgGene.c
  • lines changed 5, context: html, text, full: html, text
    8a16a63280f05173a8a843e586012199b9104f77 Mon Feb 8 14:48:02 2021 -0800
    tweaking Gencode Genes search
• src/hg/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    56069e49520647ff3c5e9c7ba63d21a39d29352d Mon Feb 15 02:53:32 2021 -0800
    change after code review, refs #26951
• src/hg/hgTracks/barChartTrack.c
  • lines changed 79, context: html, text, full: html, text
    4b572c8e95475106bbaf594bca1907c42bfb02fd Sat Jan 23 11:44:41 2021 -0800
    First cut of barChartFitGene to look at. Showing correct colors and bars and stretching. Getting spacing between bars in still to be done and some other things, but it's looking good in a lot of ways. Will let us zoom into the bars for sure anyway.
  • lines changed 85, context: html, text, full: html, text
    3b51940eefa1013e69a0d3bbd18855aeec472855 Sat Jan 23 17:43:48 2021 -0800
    Adding mapBoxes and a little spacing between bars once zoomed in enough. Removed a bunch of unneeded casts.
  • lines changed 31, context: html, text, full: html, text
    b37fd074677d8316e79536f2755106cf50ba2b8b Sun Jan 24 12:02:07 2021 -0800
    Making dense/squish behavior same as old barChart since it already is proportional. Making the squish mode's notion of tissue specificity scale to a greater or lesser number of bars in a somewhat sensible way while maintaining compatibility with GTEX in 54 bar case.
  • lines changed 1, context: html, text, full: html, text
    58f0d8c948e3e9de535d52854d58c11950eae8ce Thu Jan 28 18:01:03 2021 -0800
    Removing an unused define.
  • lines changed 55, context: html, text, full: html, text
    f7ae366edc0250eb4f61b52bc065ddbe6fa55cfd Sat Jan 30 14:16:21 2021 -0800
    Making proportional bars respect selected categories, and setting categories from facets, so what gets drawn reflects what facets are selected in faceted mode.
  • lines changed 193, context: html, text, full: html, text
    a693e3b71a0933e2cb6ea62dcb571b8a6a53a17e Tue Feb 2 11:23:21 2021 -0800
    Quite a bit of refactoring including removing a redundant routine, countFilteredBars. Functionally added two things: a new level of zoom out on the bar chart display (non-fit-to-gene case) and apply filters before doing width calculations so that your bars can get wider when you filter things out.
  • lines changed 102, context: html, text, full: html, text
    d4ea24a2fedb651ffefbab4095c25eb9d1be8db3 Tue Feb 2 17:52:52 2021 -0800
    I think I got it working in a way that combines best of the proportional and non-proportional ways, and it even seems to work in multi-region!
  • lines changed 146, context: html, text, full: html, text
    4f14572c392ef39b38df827df7adba1a36a75cd1 Wed Feb 3 08:21:48 2021 -0800
    Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code.
  • lines changed 2, context: html, text, full: html, text
    683e3d036a593d3742c5b7669876e0f6babd206e Wed Feb 3 09:56:44 2021 -0800
    Made map box extend just a little over the bars for easier mouse-overs, and especially to read categories of empty bars.
• src/hg/hgTracks/wigTrack.c
  • lines changed 7, context: html, text, full: html, text
    5634a1ee547d0d332bfe1ec37e164bfe896d6288 Mon Feb 8 17:23:03 2021 -0800
    honor the log transform and the negate option for mouseOver values refs #26505
  • lines changed 5, context: html, text, full: html, text
    481c4c69ad6d397389245f52c0da1477ab8703b1 Wed Feb 10 14:12:54 2021 -0800
    do NOT do log transform for mouse over value refs #26505
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    0c54fc14a14f7258dd59e88911e4385c02032a4d Sat Jan 23 17:41:05 2021 -0800
    Slightly tweaking estimated size.
  • lines changed 2, context: html, text, full: html, text
    5a4b3dd2b0a854d819f473d1c891cd7f27a6f76a Thu Jan 28 10:32:56 2021 -0800
    Improving label, using barChartLabel from trackDb if available in place of 'Sample'
  • lines changed 29, context: html, text, full: html, text
    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
• src/hg/hgc/facetedBar.c
  • lines changed 328, context: html, text, full: html, text
    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
  • lines changed 215, context: html, text, full: html, text
    26a38dbb5ff226e6848067217518ff9e212696b8 Sat Jan 30 11:43:20 2021 -0800
    Refactoring facetedTable stuff from a hgc module into a library routine.
  • lines changed 3, context: html, text, full: html, text
    7f165a4c474605452621918390c40378a571eec5 Sun Jan 31 08:31:08 2021 -0800
    Getting the facets properly (not in an iFrame) into hgTrackUi.
  • lines changed 1, context: html, text, full: html, text
    fd94d0a12db7f77ea6febd8f31c4bbf40558e692 Mon Feb 1 17:26:33 2021 -0800
    Reducing size of facet all the way down to 5.
• src/hg/hgc/facetedBar.h
  • lines changed 3, context: html, text, full: html, text
    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
• src/hg/htdocs/cite.html
  • lines changed 2, context: html, text, full: html, text
    04ddbe89cbeb3fbc9286b8e1f1a47b949e1d3934 Tue Feb 9 14:22:19 2021 -0800
    Adding a note about permissions for using images generated by the Genome Browser, refs #26915
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 63, context: html, text, full: html, text
    2ff8201b43ce7f5a9f66c9bf81842ba9f5002b75 Wed Feb 10 17:54:02 2021 -0800
    Doc'ing new defaultCart feature for GBiB. Also removed a note about a broken link, the link is only broken since it leads to a local GBiB. It works as expected if there is a GBiB running. refs #26938
• src/hg/htdocs/inc/gbFooter.html
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    08e43217f8619a1eb3d603186e4521bee16c5217 Wed Feb 10 13:14:39 2021 -0800
    changed copyright info. update 2020 to 2021
• src/hg/htdocs/inc/gbFooterHardcoded.html
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    08e43217f8619a1eb3d603186e4521bee16c5217 Wed Feb 10 13:14:39 2021 -0800
    changed copyright info. update 2020 to 2021
• src/hg/htdocs/inc/gbsFooter.html
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    08e43217f8619a1eb3d603186e4521bee16c5217 Wed Feb 10 13:14:39 2021 -0800
    changed copyright info. update 2020 to 2021
• src/hg/htdocs/inc/jWestFooter.html
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    08e43217f8619a1eb3d603186e4521bee16c5217 Wed Feb 10 13:14:39 2021 -0800
    changed copyright info. update 2020 to 2021
• src/hg/htdocs/license/index.html
  • lines changed 6, context: html, text, full: html, text
    04ddbe89cbeb3fbc9286b8e1f1a47b949e1d3934 Tue Feb 9 14:22:19 2021 -0800
    Adding a note about permissions for using images generated by the Genome Browser, refs #26915
• src/hg/htdocs/style/facets.css
  • lines changed 18, context: html, text, full: html, text
    eee321cc5afaeee3de0eae87328ef0a95ad97206 Wed Jan 27 12:42:59 2021 -0800
    Attempting to import just enough style to support the faceted search in tableTables without bringing in all of CIRM.
  • lines changed 9, context: html, text, full: html, text
    f031e7b2f184a8e6d5f19fa86dee46f4574f16ad Fri Jan 29 22:06:43 2021 -0800
    Adding a few more things to make facets look nicer on genome browser details pages.
  • lines changed 4, context: html, text, full: html, text
    0c11f4b452d602430c58985896098e18762792c2 Sat Jan 30 08:57:56 2021 -0800
    Overriding dark gray background on facet's buttons.
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    eee321cc5afaeee3de0eae87328ef0a95ad97206 Wed Jan 27 12:42:59 2021 -0800
    Attempting to import just enough style to support the faceted search in tableTables without bringing in all of CIRM.
• src/hg/htdocs/training/index.html
  • lines changed 24, context: html, text, full: html, text
    a21b919538ca05d4b3380b28ac426b67873c15dd Tue Feb 9 17:02:05 2021 -0800
    removed completed oregon, city of hope and ucla workshops. added mckusick. fixed some links
  • lines changed 1, context: html, text, full: html, text
    3fd938e98028071936bc7fee8032778aafb51d94 Tue Feb 9 17:27:58 2021 -0800
    removed errant line
• src/hg/inc/barChartUi.h
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    774bbb884b2db8ab3e314c08a42bef1436a6977c Sat Jan 23 17:40:14 2021 -0800
    Adding a define for a tdb setting as seems the style here.
  • lines changed 4, context: html, text, full: html, text
    8c4164e0b5c848c3b9f8103ac8715ba851823bf9 Wed Feb 3 08:10:14 2021 -0800
    Increasing max categories to 2000 since 1000 looks like may happen in a year. Removing unused define.
• src/hg/inc/facetField.h
  • lines changed 2, context: html, text, full: html, text
    a93fb7921260a5c8555bfe3a9f63acec910028e3 Thu Jan 28 18:03:09 2021 -0800
    Turning a define into facetUsualSize parameter, so it's not always 20 any more! Improving commenting of webFilteredSqlTable function.
  • lines changed 5, context: html, text, full: html, text
    fe1627a44ee54d0dcffd8cdd27d31f499ca6d5f6 Fri Jan 29 16:08:16 2021 -0800
    Adding a function that is helpful when using facets on memory tables.
  • lines changed 6, context: html, text, full: html, text
    64cf5265a375948af55b9237cd3fd91f8749f0e2 Sat Jan 30 08:56:53 2021 -0800
    Making facetFieldsFromFieldedTable return the subtable that it has selected out, which is a bit more useful.
• src/hg/inc/facetedTable.h
  • lines changed 55, context: html, text, full: html, text
    26a38dbb5ff226e6848067217518ff9e212696b8 Sat Jan 30 11:43:20 2021 -0800
    Refactoring facetedTable stuff from a hgc module into a library routine.
  • lines changed 13, context: html, text, full: html, text
    ac7eb539eddf7c733a2319d409807d3d5f126bdc Mon Feb 1 17:25:34 2021 -0800
    Improved commenting.
• src/hg/inc/hgColors.h
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    6fb8c54f1cc0175c8b913c098ff4f5fb91ba7714 Sat Jan 30 11:45:29 2021 -0800
    Added a routine that'll turn the inside of our formatting tables from cream to white.
• src/hg/inc/tablesTables.h
  • lines changed 24, context: html, text, full: html, text
    a93fb7921260a5c8555bfe3a9f63acec910028e3 Thu Jan 28 18:03:09 2021 -0800
    Turning a define into facetUsualSize parameter, so it's not always 20 any more! Improving commenting of webFilteredSqlTable function.
• src/hg/lib/barChartUi.c
  • lines changed 24, context: html, text, full: html, text
    0b58f51e038bbae5f53aecbed905b7e959b08d84 Thu Jan 28 18:05:34 2021 -0800
    Starting to add a new UI involving facets for the wide bar charts. It is not under hg.conf control, but currently only triggers for a track named 'singleCellMerged'
  • lines changed 81, context: html, text, full: html, text
    7f165a4c474605452621918390c40378a571eec5 Sun Jan 31 08:31:08 2021 -0800
    Getting the facets properly (not in an iFrame) into hgTrackUi.
• src/hg/lib/facetField.c
  • lines changed 34, context: html, text, full: html, text
    fe1627a44ee54d0dcffd8cdd27d31f499ca6d5f6 Fri Jan 29 16:08:16 2021 -0800
    Adding a function that is helpful when using facets on memory tables.
  • lines changed 16, context: html, text, full: html, text
    64cf5265a375948af55b9237cd3fd91f8749f0e2 Sat Jan 30 08:56:53 2021 -0800
    Making facetFieldsFromFieldedTable return the subtable that it has selected out, which is a bit more useful.
• src/hg/lib/facetedTable.c
  • lines changed 196, context: html, text, full: html, text
    26a38dbb5ff226e6848067217518ff9e212696b8 Sat Jan 30 11:43:20 2021 -0800
    Refactoring facetedTable stuff from a hgc module into a library routine.
  • lines changed 2, context: html, text, full: html, text
    ac7eb539eddf7c733a2319d409807d3d5f126bdc Mon Feb 1 17:25:34 2021 -0800
    Improved commenting.
• src/hg/lib/hgColors.c
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    6fb8c54f1cc0175c8b913c098ff4f5fb91ba7714 Sat Jan 30 11:45:29 2021 -0800
    Added a routine that'll turn the inside of our formatting tables from cream to white.
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    26a38dbb5ff226e6848067217518ff9e212696b8 Sat Jan 30 11:43:20 2021 -0800
    Refactoring facetedTable stuff from a hgc module into a library routine.
• src/hg/lib/tablesTables.c
  • lines changed 155, context: html, text, full: html, text
    0002cfbdde2e145cf945fba9a26c6e60ea3cd666 Thu Jan 28 18:08:55 2021 -0800
    Quite a bit of refactoring to help make this work inside a genome browser page. Still a bit to go. In particular have made the facet count a parameter, and have made the buttons associated with a search optional to display. Also facets no longer have to be visible fields. I'm hoping I have not broken CIRM CDW compatibility but have not tested sufficiently.
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    81f240f86b16d599cafde436527c5a6a6b87e456 Thu Jan 28 20:59:17 2021 -0800
    getting rid of a lot of hard coded cdwBrowseFiles where prefixVar should be used. Making it not need a submit button for paging to work.
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    f696e3739df240549d0ef2a172a13f7b4d2a8433 Thu Jan 28 21:26:51 2021 -0800
    Making facet_op be not hard coded
  • lines changed 20, context: html, text, full: html, text
    dacec81196967c10d494c7b77a49cc41a5aa63ce Thu Jan 28 22:10:56 2021 -0800
    Making a couple of more variables use the varPrefix rather than be hard coded.
  • lines changed 12, context: html, text, full: html, text
    19e6e03d64ce54f9db60a93734cd3b573eb0446b Fri Jan 29 09:07:37 2021 -0800
    I believe I got all the faceted variables using the varPrefix. Tested this by having two faceted tables on the same page and it worked. Looks clean by cartDump too.
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    0404d37052e75524e84f894da06786c45426e6b6 Fri Jan 29 16:09:10 2021 -0800
    Fixing a case-mismatch typo that broke checkboxes.
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    13e3bdbc4767d3dc557c9921e56d81c115767a32 Mon Feb 1 16:11:15 2021 -0800
    Adding some anchors and IDs so that when select a facet it will tend to come back to about where you were in the page rather than popping you back up to the top.
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    4ccbe6b36f3a9fdd09c08ad21efa19d20cb593a0 Wed Feb 3 08:11:46 2021 -0800
    Making it issue anchors only every 15 items in a list. This results in a bit less jumping.
• src/hg/lib/trackDbCache.c
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    9bab4c39709d774c2a439dc8b5776b451510bef4 Wed Feb 10 11:53:57 2021 -0800
    delete the incFiles.txt file if there aren't any include files in the cached trackDb
• src/hg/lib/web.c
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    52f71c2ffebe8fa15d6c5af0b6eeb854cd4723f1 Sat Jan 30 08:54:25 2021 -0800
    Adding hgInside class to tables-for-color-and-layout that are colored HC_COL_INSIDE so can override the style as one more step away from cream colored backgrounds.
• src/hg/makeDb/cadd/cadd.as
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    0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800
    adding makedoc for cadd track, refs #18492
• src/hg/makeDb/cadd/caddToBed.py
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    0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800
    adding makedoc for cadd track, refs #18492
• src/hg/makeDb/cadd/caddToWig.py
  • lines changed 63, context: html, text, full: html, text
    0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800
    adding makedoc for cadd track, refs #18492
• src/hg/makeDb/doc/hg19.txt
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    0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800
    adding makedoc for cadd track, refs #18492
• src/hg/makeDb/doc/hg38/cadd.txt
  • lines changed 14, context: html, text, full: html, text
    0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800
    adding makedoc for cadd track, refs #18492
• src/hg/makeDb/doc/mm39/lastzRuns.txt
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    4efd040664982d940ec8244cacb18724c08ac64f Mon Feb 8 14:04:43 2021 -0800
    add the make procedure for the assembly hub chainNet runs refs #26815
• src/hg/makeDb/schema/all.joiner
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    b9f2d3c69ed82b01ee86bf36995abe72e8926be3 Mon Feb 8 12:33:18 2021 -0800
    add to chainDest list dbs used in mm39 chainNets refs #26815
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    5c7ce8dbc0e4a3c5bfd55a08ad44b9fb60704aa9 Mon Feb 8 14:02:31 2021 -0800
    adding PanPan3 to the non-self chain list refs #26815
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    50d8ee9d40c249470a706bfa94dccfca19364707 Tue Feb 9 09:07:22 2021 -0800
    adding docs page for CADD track, refs #18492
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    27b2e604eca2e8a1924ea26059869f1efc5d7efb Tue Feb 9 12:54:11 2021 -0800
    Changing AF mouseover from gnomAD refs #26835
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    62763f72d693a15e1ed449c8aaf28d611a7b3e15 Thu Jan 28 18:10:38 2021 -0800
    Adding the new barChartFitGene setting and moving the type up a level.
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    4f14572c392ef39b38df827df7adba1a36a75cd1 Wed Feb 3 08:21:48 2021 -0800
    Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code.
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    3f580c1f91f06a09d3041db544195a741fdab6bf Mon Feb 8 12:57:14 2021 -0800
    Adding facets.
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    27b2e604eca2e8a1924ea26059869f1efc5d7efb Tue Feb 9 12:54:11 2021 -0800
    Changing AF mouseover from gnomAD refs #26835
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    8a16a63280f05173a8a843e586012199b9104f77 Mon Feb 8 14:48:02 2021 -0800
    tweaking Gencode Genes search
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    8aceeebf936e297352f6f40f5af220e596662143 Sat Jan 23 17:17:10 2021 -0800
    Improving labels and enabling proportional-to-gene-size scaling
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    8f1759486dc4a97ce0a9640913dffd4579e71e20 Thu Jan 28 18:11:41 2021 -0800
    Adding some experimental stanzas and tweaking labels
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    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
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    0a552251d95d38c782e072dadfedb409134be5a1 Mon Feb 1 17:30:47 2021 -0800
    Moving to using the normalized version by default.
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    4f14572c392ef39b38df827df7adba1a36a75cd1 Wed Feb 3 08:21:48 2021 -0800
    Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code.
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    ca38bbbd964d836fc9be34323765aa8dc035a67a Sat Jan 23 17:49:08 2021 -0800
    Moving single cell tracks to a new singleCell group. Better labels for the merged track barcharts.
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    cd33851b670a3fbf2dce528ee1d623768a421004 Mon Feb 8 12:58:50 2021 -0800
    Starting work on another lung set.
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    4bf5a18faecd1f3fe855e2b82e442bae31fb819a Mon Feb 8 13:00:58 2021 -0800
    Merge branch 'jimk_singleCellMerged'. This brings in faceted search in the barcharts mostly. It also changes the way that the barcharts work in hgTracks. There are two new levels of display - one when zoomed far out that lets the barcharts get skinnier one more level, and another when zoomed in to the point where the gene is wide enough to host the whole chart. At this point the chart starts sticking in scale proportionally in a continuous fashion to the gene, so zooming in on a section of the chart is done the same way that zooming in on a section of the gene is.
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.ra
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
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    c3aaccb090dee84beeaece8be9f9ea10409e68dd Wed Feb 10 10:45:08 2021 -0800
    Fixing extra slash on link, caused track not to appear on beta/RR. No RM.
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    170405c69537a1aaa09398437a3f13cc93811aa1 Sat Jan 23 17:47:01 2021 -0800
    Adding explicitly that GTEX is not trying to fitToGene.
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    4f14572c392ef39b38df827df7adba1a36a75cd1 Wed Feb 3 08:21:48 2021 -0800
    Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code.
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
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    75c824ea4938854f1c48795b50f06de2140fd4b4 Fri Feb 12 09:50:37 2021 -0800
    Editing the matrix and minScore for the macFas5 chain/net for marmoset, refs #24074
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    3b1dae8699519cfd00b324c4b92b13d0918440a9 Fri Feb 12 13:24:23 2021 -0800
    Staging the refseq composite track on beta, refs #24074
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM10.ra
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
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    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM12.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM13.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM16.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM18.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM21.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM22.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM23.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra
  • lines changed 22, context: html, text, full: html, text
    b3dd719260e5f6b3a9f3983dfca0ac870f108e67 Mon Feb 8 16:27:11 2021 -0800
    Disable gene symbol searches for all but the latest ALL GENCODE track, refs eng-meeting Feb 8 2021
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d36b68a1f3a42cb884d1b74f3c321429f4a132e4 Fri Feb 12 13:48:05 2021 -0800
    syntenic and rbest chain/net should have tag alpha refs #26584
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    dd1fb0ead6727cfaf6988b4ededcc4f484ccd99d Sat Jan 23 17:45:21 2021 -0800
    Adding barChartFitGene tag
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    038e590eac583c4253e53b234b365a4e842586c5 Sat Jan 30 09:02:52 2021 -0800
    Initial implementation of barChartFacet feature in click display.
  • lines changed 1, context: html, text, full: html, text
    4f14572c392ef39b38df827df7adba1a36a75cd1 Wed Feb 3 08:21:48 2021 -0800
    Removing barChartFitGene tag and associated code since have integrated the best part of it into the existing code.
• src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra
  • lines changed 96, context: html, text, full: html, text
    8cb6022fe5989ba33bb99a553adb9902083ebea2 Wed Feb 10 13:24:51 2021 -0800
    First cut strains track from alignments of GISAID seqs by Nick Keener, with direction from Angie. refs #26876
  • lines changed 1, context: html, text, full: html, text
    3f9969b5073ecebea3f0474a1302ac6dc3ad7688 Thu Feb 11 05:23:16 2021 -0800
    changing default tracks for wuhCor1, email from Kate
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c430735037fc90307fec1f071ac7cd61d2b9963b Thu Feb 11 18:55:29 2021 -0800
    Simplify Variants of Concern track config. refs #27876
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    27a1a4a6bcedbb88258842b0e88024bfe7a57cc0 Thu Feb 11 19:00:31 2021 -0800
    Minor trackDb tweaks. refs #26876
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 8, context: html, text, full: html, text
    c3431e6dc17aa3c520229701ae73af03786d3ed7 Fri Feb 12 02:52:11 2021 -0800
    hiding wuhCor1 protease tracks, email from Kate, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 174, context: html, text, full: html, text
    0f3bebf8b89a0cd3a9fa05e143cde0f7d5cd8294 Thu Feb 11 18:36:29 2021 -0800
    Expand and polish track description. refs #26876
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 111, context: html, text, full: html, text
    b5fbe1f931477e0b1606c28a3d020286eb3a4fb0 Wed Feb 10 14:22:05 2021 -0800
    Update variants of interest track config. refs #26876
  • lines changed 120, context: html, text, full: html, text
    b7cd393ba3a1ac68e2ded67ec953d4eea8f95f94 Thu Feb 11 18:37:33 2021 -0800
    Polish trakc labels and config. refs #26876
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    c430735037fc90307fec1f071ac7cd61d2b9963b Thu Feb 11 18:55:29 2021 -0800
    Simplify Variants of Concern track config. refs #27876
  • lines changed 1, context: html, text, full: html, text
    27a1a4a6bcedbb88258842b0e88024bfe7a57cc0 Thu Feb 11 19:00:31 2021 -0800
    Minor trackDb tweaks. refs #26876
• src/hg/makeDb/trackDb/virus/wuhCor1/weizmanOrfs.ra
  • lines changed 1, context: html, text, full: html, text
    6b3051540d38f212e231b7cfb37bed56c38cdb58 Fri Feb 12 02:58:02 2021 -0800
    tweaking wuhCor1 Weizman a little
• src/hg/oneShot/hgFacetedBars/hgFacetedBars.c
  • lines changed 166, context: html, text, full: html, text
    2f6acb208e6abe1f09be24d4a6bec948148a5ee9 Mon Feb 1 17:29:10 2021 -0800
    Moving this to directory for exploratory non-reviewed code. It was a nice little platform to work out ideas.
• src/hg/oneShot/hgFacetedBars/makefile
  • lines changed 18, context: html, text, full: html, text
    2f6acb208e6abe1f09be24d4a6bec948148a5ee9 Mon Feb 1 17:29:10 2021 -0800
    Moving this to directory for exploratory non-reviewed code. It was a nice little platform to work out ideas.
• src/hg/utils/automation/doNcbiRefSeq.pl
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    ade27c29a043212fc5b09a6f767e5dac6063a1ce Wed Feb 10 15:28:58 2021 -0800
    correctly adding symlinks to goldenPath bigZips genes directory no redmine
• src/inc/fieldedTable.h
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    6b80663a8dd1cfde9d076fa09ff3cecbec527035 Sat Jan 30 11:46:34 2021 -0800
    Added routine that will calc max of items in a column since it might be reusued.
• src/inc/hex.h
  • lines changed 3, context: html, text, full: html, text
    b85edc2f33f9958930fc36dc3f9ba154b6b631b1 Mon Feb 1 17:24:03 2021 -0800
    Adding unpackHexString function to library.
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    99360b369879974f4ad62dcc52d41ce98f616a46 Wed Feb 3 08:22:31 2021 -0800
    Adding an include dependency.
• src/lib/fieldedTable.c
  • lines changed 22, context: html, text, full: html, text
    6b80663a8dd1cfde9d076fa09ff3cecbec527035 Sat Jan 30 11:46:34 2021 -0800
    Added routine that will calc max of items in a column since it might be reusued.
• src/lib/hex.c
  • lines changed 34, context: html, text, full: html, text
    aef030e99fe05f80367079483c7b15367d5b2b16 Mon Feb 1 09:34:09 2021 -0800
    Moving unpackHexString to library per code review #26824
• src/lib/tabRow.c
  • lines changed 1, context: html, text, full: html, text
    0dd8644e032ab5f31e2ac74379db400ccaef5382 Mon Jan 25 16:36:48 2021 -0800
    Fixed reversal bug #26863
• src/product/README.building.source
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    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.cram
  • lines changed 54, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.customTracks.dataBase
  • lines changed 230, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.install
  • lines changed 229, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.mysql.setup
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    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.proxy
  • lines changed 40, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.requirements
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    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.trackDb
  • lines changed 150, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/README.udc
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    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/product/mirrorManual.txt
  • lines changed 331, context: html, text, full: html, text
    295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800
    changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
• src/utils/chromToUcsc/chromToUcsc
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    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/chromToUcsc/tests/expected/mm10.gtf
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    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/chromToUcsc/tests/in/grc38.100.gtf.gz
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    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/qa/weeklybld/buildEnv.csh
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    ff5a87a48e128432c4b35b1eb1dc671d1bbde7c1 Mon Feb 15 10:20:49 2021 -0800
    v411 preview1, refs #26867
• src/utils/qa/weeklybld/makeStrictBeta.csh
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    dd14a53519dd33f8bb4c3b65897b5cfafc42b2c7 Mon Feb 8 14:54:47 2021 -0800
    ignore ignored errors
• src/utils/rowsToCols/tests/expected/tab
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    aea6736de0c77ce1badd2c0f66344d5e279d16dd Mon Jan 25 16:39:37 2021 -0800
    Updating test case, which just confirmed broken behavior.
• src/utils/userApps/fetchChromSizes
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    69485aeccc760b6d9db9e6ed6be817272f279635 Sat Feb 13 03:23:32 2021 -0800
    fixing fetchChromSizes for hg19-hg38 patch levels, no redmine, email from Beagon/Ana

• lines changed: 7563
• files changed: 221