Commits for hiram

v427_base to v428_preview (2022-02-21 to 2022-02-28) v428

b1d778892148961ead898fc47ff04c594c1f2ad6 Fri Feb 18 11:53:16 2022 -0800

• do not overwrite index.html until it is finished and reinstate size limit filter and correctly sort the submitter column refs #28930
  • src/hg/gar/rebuild.sh - lines changed 3, context: html, text, full: html, text

b2de9d458c5a1afbcb1eda2ee6d636e2fbc21c76 Mon Feb 21 15:04:36 2022 -0800

• correctly use specified index file for cram file types no redmine
  • src/lib/bamFile.c - lines changed 5, context: html, text, full: html, text

d4fdeadb1c734b4bf4d9885f462fa93c79df55b7 Mon Feb 21 16:02:14 2022 -0800

• add tooltip doc on column headers refs #28930
  • src/hg/gar/garTable.pl - lines changed 53, context: html, text, full: html, text
  • src/hg/htdocs/style/gar.css - lines changed 63, context: html, text, full: html, text

369fd3ec5b7eaf247fd3da2c8c9377a474161c14 Tue Feb 22 10:34:33 2022 -0800

• fixup correct text for content on filled-in form fields refs #28930
  • src/hg/js/gar.js - lines changed 4, context: html, text, full: html, text

942526536cf6261f16915b8c8c127829d70be133 Tue Feb 22 13:14:24 2022 -0800

• rework the content of the introduction text refs #28930
  • src/hg/gar/garTable.sh - lines changed 62, context: html, text, full: html, text

28bb2659b7500bceab10a942b68bbbea26f56d2a Tue Feb 22 13:15:40 2022 -0800

• extend the all argument to also turn on all rows refs #28930
  • src/hg/js/gar.js - lines changed 5, context: html, text, full: html, text

f9d9bdc8e2612f9478370a867a4216fb3b0cf345 Tue Feb 22 13:17:05 2022 -0800

• clean up unused rules and add box shadows around the pull-down menu boxes refs #28930
  • src/hg/htdocs/style/gar.css - lines changed 153, context: html, text, full: html, text

6647ae199221972aa0fbd68d015f80aa0aeef58a Tue Feb 22 13:59:33 2022 -0800

• center the pull down menu anchor text refs #28930
  • src/hg/htdocs/style/gar.css - lines changed 2, context: html, text, full: html, text

98e1f23b286fccc2636e7cdeadb3c5cd1c936876 Tue Feb 22 14:00:08 2022 -0800

• change text on column hide show pull down manu refs #28930
  • src/hg/gar/garTable.pl - lines changed 2, context: html, text, full: html, text

2cf3578abce882ea76c4d4f1309972a07797ba4f Tue Feb 22 14:29:18 2022 -0800

• better cleaning of sort keys for submitter strings and h1 h2 headings on intro text refs #28930
  • src/hg/gar/garTable.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 5, context: html, text, full: html, text

53902497740c6def14977a0c32a0dc95765b0307 Tue Feb 22 19:57:35 2022 -0800

• adding assembly GCA_013030995.1_ASM1303099v1 per user request refs #28954
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

8678a6ea54cde92af856614a789fc353b2dbd8e8 Tue Feb 22 20:00:22 2022 -0800

• adding assembly GCA_013030995.1_ASM1303099v1 per user request refs #28954
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text

1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 Thu Feb 24 14:05:28 2022 -0800

• add a column 1 tool tip to indicate request or browser refs #28930
  • src/hg/gar/garTable.pl - lines changed 17, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/style/gar.css - lines changed 21, context: html, text, full: html, text
  • src/hg/js/gar.js - lines changed 45, context: html, text, full: html, text

dcc09e71de2cb1f61a19f0526e0595ceb8277bb3 Fri Feb 25 10:43:00 2022 -0800

• adding cell background coloring for the IUCN column and tri-state indication on the hideAll buttons refs #28930
  • src/hg/gar/garTable.pl - lines changed 22, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/style/gar.css - lines changed 36, context: html, text, full: html, text
  • src/hg/js/gar.js - lines changed 6, context: html, text, full: html, text

980a640fde4cdcd5aa34f24de2f71e51e3d0fe61 Fri Feb 25 10:50:52 2022 -0800

• stalled on cpgIslands refs #23367
  • src/hg/makeDb/doc/ambMex2/initialBuild.txt - lines changed 5, context: html, text, full: html, text

c0a4905df836349697fb24147e35cf5b7f737a09 Fri Feb 25 10:54:49 2022 -0800

• lastz galGal6 to GCF_016699485.2 per user request refs #28336
  • src/hg/makeDb/doc/galGal6/lastzRuns.txt - lines changed 95, context: html, text, full: html, text

3b2dda0ff5910870d3279ffe52d987d5c5a7bb64 Fri Feb 25 10:55:54 2022 -0800

• phyloP experiment with SSREV parameter per user request no redmine
  • src/hg/makeDb/doc/hg38/multiz30way.txt - lines changed 323, context: html, text, full: html, text

92caabd2ff459cd75f8b5451f9d0f7fa5043d3b9 Fri Feb 25 10:58:18 2022 -0800

• finished lastz to bosTau9 no redmine
  • src/hg/makeDb/doc/rn7/lastzRuns.txt - lines changed 17, context: html, text, full: html, text

a1e6ba20edee50a0a5380524d26a89968292f47b Fri Feb 25 10:59:53 2022 -0800

• experiment with phyloP with SSREV parameters per user request no redmine
  • src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra - lines changed 19, context: html, text, full: html, text

e78b1f8b7121149606b00890d327b78c06cd2522 Fri Feb 25 11:01:10 2022 -0800

• cleaner determination of genBankAccession no redmine
  • src/hg/utils/automation/prepConfig.pl - lines changed 2, context: html, text, full: html, text

3ab681f0f137f69e14917a4cb67cf21dd923b2e3 Fri Feb 25 11:01:53 2022 -0800

• update a couple of identities to newer versions no redmine
  • src/hg/utils/phyloTrees/220way.nh - lines changed 11, context: html, text, full: html, text

af7a004c8f3fa909cd8c2cfc2e5bea60e3421cd1 Fri Feb 25 11:02:46 2022 -0800

• cleaner determination of parameters no redmine
  • src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl - lines changed 55, context: html, text, full: html, text

8068dd517b970501ce9b10759142e0aa24e3102f Fri Feb 25 15:37:57 2022 -0800

• adding two new columns for bioSample and bioProject refs #28930
  • src/hg/htdocs/style/gar.css - lines changed 12, context: html, text, full: html, text

e56876e545b21501152e96f655141eb3b229cf0c Fri Feb 25 16:19:26 2022 -0800

• add in bioSample and bioProject columns and control of IUCN display refs #28930
  • src/hg/gar/garTable.pl - lines changed 44, context: html, text, full: html, text
  • src/hg/js/gar.js - lines changed 13, context: html, text, full: html, text