Commits for kent

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

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.
  • src/hg/hgTracks/barChartTrack.c - lines changed 79, context: html, text, full: html, text

8aceeebf936e297352f6f40f5af220e596662143 Sat Jan 23 17:17:10 2021 -0800

• Improving labels and enabling proportional-to-gene-size scaling
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 7, context: html, text, full: html, text

774bbb884b2db8ab3e314c08a42bef1436a6977c Sat Jan 23 17:40:14 2021 -0800

• Adding a define for a tdb setting as seems the style here.
  • src/hg/inc/barChartUi.h - lines changed 3, context: html, text, full: html, text

0c54fc14a14f7258dd59e88911e4385c02032a4d Sat Jan 23 17:41:05 2021 -0800

• Slightly tweaking estimated size.
  • src/hg/hgc/barChartClick.c - lines changed 1, 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.
  • src/hg/hgTracks/barChartTrack.c - lines changed 85, context: html, text, full: html, text

dd1fb0ead6727cfaf6988b4ededcc4f484ccd99d Sat Jan 23 17:45:21 2021 -0800

• Adding barChartFitGene tag
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

170405c69537a1aaa09398437a3f13cc93811aa1 Sat Jan 23 17:47:01 2021 -0800

• Adding explicitly that GTEX is not trying to fitToGene.
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 3, context: html, text, full: html, text

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/bloodHao.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/colonWang.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ileumWang.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/lungVieiraBraga.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rectumWang.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra - lines changed 1, 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.
  • src/hg/hgTracks/barChartTrack.c - lines changed 31, context: html, text, full: html, text

0dd8644e032ab5f31e2ac74379db400ccaef5382 Mon Jan 25 16:36:48 2021 -0800

• Fixed reversal bug #26863
  • src/lib/tabRow.c - lines changed 1, context: html, text, full: html, text

aea6736de0c77ce1badd2c0f66344d5e279d16dd Mon Jan 25 16:39:37 2021 -0800

• Updating test case, which just confirmed broken behavior.
  • src/utils/rowsToCols/tests/expected/tab - 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/style/facets.css - lines changed 18, context: html, text, full: html, text
  • src/hg/htdocs/style/makefile - lines changed 2, 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.
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 120, context: html, text, full: html, text
  • src/hg/hgFacetedBars/makefile - lines changed 18, 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'
  • src/hg/hgc/barChartClick.c - lines changed 2, 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.
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 31, context: html, text, full: html, text

01212f5c7964f242897e015217ba2a149f5c23bf Thu Jan 28 17:54:31 2021 -0800

• Reducing facet size to 15
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text

58f0d8c948e3e9de535d52854d58c11950eae8ce Thu Jan 28 18:01:03 2021 -0800

• Removing an unused define.
  • src/hg/hgTracks/barChartTrack.c - lines changed 1, 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/inc/facetField.h - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/tablesTables.h - 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'
  • src/hg/lib/barChartUi.c - lines changed 24, 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.
  • src/hg/lib/tablesTables.c - lines changed 155, context: html, text, full: html, text

62763f72d693a15e1ed449c8aaf28d611a7b3e15 Thu Jan 28 18:10:38 2021 -0800

• Adding the new barChartFitGene setting and moving the type up a level.
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 10, context: html, text, full: html, text

8f1759486dc4a97ce0a9640913dffd4579e71e20 Thu Jan 28 18:11:41 2021 -0800

• Adding some experimental stanzas and tweaking labels
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 40, context: html, text, full: html, text

fc400c236d017af4a7f530cfdbfefbc3bc08f3f9 Thu Jan 28 18:15:34 2021 -0800

• Merge branch 'master' into jimk_singleCellMerged so as to keep up with other people's changes.

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.
  • src/hg/lib/tablesTables.c - lines changed 39, context: html, text, full: html, text

f696e3739df240549d0ef2a172a13f7b4d2a8433 Thu Jan 28 21:26:51 2021 -0800

• Making facet_op be not hard coded
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 12, 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.
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 89, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 20, 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/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 68, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 12, 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.
  • src/hg/inc/facetField.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/facetField.c - lines changed 34, context: html, text, full: html, text

0404d37052e75524e84f894da06786c45426e6b6 Fri Jan 29 16:09:10 2021 -0800

• Fixing a case-mismatch typo that broke checkboxes.
  • src/hg/lib/tablesTables.c - lines changed 1, 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.
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 38, 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.
  • src/hg/htdocs/style/facets.css - lines changed 9, context: html, text, full: html, text

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/lib/web.c - lines changed 2, 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/facetField.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/facetField.c - lines changed 16, 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/facets.css - lines changed 4, 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/barChartClick.c - lines changed 29, context: html, text, full: html, text
  • src/hg/hgc/facetedBar.c - lines changed 328, context: html, text, full: html, text
  • src/hg/hgc/facetedBar.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgc/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, 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.
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 111, 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/hgc/facetedBar.c - lines changed 215, context: html, text, full: html, text
  • src/hg/inc/facetedTable.h - lines changed 55, context: html, text, full: html, text
  • src/hg/lib/facetedTable.c - lines changed 196, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 2, context: html, text, full: html, text

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/hgColors.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hgColors.c - lines changed 14, 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/inc/fieldedTable.h - lines changed 4, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 22, 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.
  • src/hg/hgTracks/barChartTrack.c - lines changed 55, 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/hgc/facetedBar.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/barChartUi.c - lines changed 81, context: html, text, full: html, text

396eb0a4fd1d3b5d41530a62a5d9719a21eace93 Mon Feb 1 09:29:26 2021 -0800

• Removed unused refCorrelate in response to code review #26824
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 21, context: html, text, full: html, text

aef030e99fe05f80367079483c7b15367d5b2b16 Mon Feb 1 09:34:09 2021 -0800

• Moving unpackHexString to library per code review #26824
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 35, context: html, text, full: html, text
  • src/lib/hex.c - lines changed 34, context: html, text, full: html, text

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.
  • src/hg/lib/tablesTables.c - lines changed 28, context: html, text, full: html, text

b85edc2f33f9958930fc36dc3f9ba154b6b631b1 Mon Feb 1 17:24:03 2021 -0800

• Adding unpackHexString function to library.
  • src/inc/hex.h - lines changed 3, context: html, text, full: html, text

ac7eb539eddf7c733a2319d409807d3d5f126bdc Mon Feb 1 17:25:34 2021 -0800

• Improved commenting.
  • src/hg/inc/facetedTable.h - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/facetedTable.c - lines changed 2, 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.c - lines changed 1, 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.
  • src/hg/hgFacetedBars/hgFacetedBars.c - lines changed 181, 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/hgFacetedBars.c - lines changed 166, context: html, text, full: html, text
  • src/hg/hgFacetedBars/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/oneShot/hgFacetedBars/hgFacetedBars.c - lines changed 166, context: html, text, full: html, text
  • src/hg/oneShot/hgFacetedBars/makefile - lines changed 18, context: html, text, full: html, text

0a552251d95d38c782e072dadfedb409134be5a1 Mon Feb 1 17:30:47 2021 -0800

• Moving to using the normalized version by default.
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 17, 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.
  • src/hg/hgTracks/barChartTrack.c - lines changed 193, 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!
  • src/hg/hgTracks/barChartTrack.c - lines changed 102, 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/barChartUi.h - lines changed 4, context: html, text, full: html, text

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/tablesTables.c - 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/hgTracks/barChartTrack.c - lines changed 146, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

99360b369879974f4ad62dcc52d41ce98f616a46 Wed Feb 3 08:22:31 2021 -0800

• Adding an include dependency.
  • src/inc/hex.h - lines changed 5, 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/barChartTrack.c - lines changed 2, context: html, text, full: html, text

3f580c1f91f06a09d3041db544195a741fdab6bf Mon Feb 8 12:57:14 2021 -0800

• Adding facets.
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 1, context: html, text, full: html, text

cd33851b670a3fbf2dce528ee1d623768a421004 Mon Feb 8 12:58:50 2021 -0800

• Starting work on another lung set.
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

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.
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text