Commits for hiram

v429_preview to v429_preview2 (2022-03-21 to 2022-03-28) v429

7f6ed181ccec7c0a8e4e8e422a15652592db62f6 Wed Mar 23 15:11:32 2022 -0700

• most recent set of corrections refs #28961
  • src/hg/gar/garTable.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/gar/rebuild.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/garModal.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/style/gar.css - lines changed 7, context: html, text, full: html, text

e1682f6a0c29bb52840fb969f636e62ef255120f Wed Mar 23 15:24:04 2022 -0700

• better clearing of the fields in the modal request form refs #28930
  • src/hg/js/gar.js - lines changed 40, context: html, text, full: html, text

1dea84ee820d50f05255371bdaaf6d7b98f220ca Wed Mar 23 17:03:10 2022 -0700

• adding construction of bigBed file for chromAlias refs #29111
  • src/hg/utils/automation/aliasBedToCt.pl - lines changed 85, context: html, text, full: html, text
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 162, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 19, context: html, text, full: html, text

0fa05b3e9ee790c70332b1fdf90724c1f7ff8d30 Thu Mar 24 12:37:28 2022 -0700

• adding gar.js to the build refs #28930
  • src/hg/js/gar.js - lines changed 1, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text

57a8f0f882e83e90b2eb0546bc84225530690689 Thu Mar 24 12:40:59 2022 -0700

• and construct the test custom track files and bigBeds refs #29111
  • src/hg/utils/automation/aliasBedToCt.pl - lines changed 22, context: html, text, full: html, text

6dc788ffecb06424dfa24f1ccae8970ecd8b9490 Thu Mar 24 13:36:11 2022 -0700

• restore alias printout when bigBed is used for alias refs #27228
  • src/hg/hgTracks/hgTracks.c - lines changed 8, context: html, text, full: html, text

cc2335c2d1f3f50ff9e1deb19172c2695db65339 Thu Mar 24 13:52:45 2022 -0700

• correctly link to chromAlias.txt instead of chromAlias.bb to display in the chromInfo page as a link to view refs #27228
  • src/hg/hgTracks/hgTracks.c - lines changed 8, context: html, text, full: html, text

2113f4ab5376a69e9169e34db99d99a6ce20f8d5 Fri Mar 25 12:05:18 2022 -0700

• better name for refSeq variable refs #29111
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 6, context: html, text, full: html, text

9f4b0740f6d6b421da7b2c8d346b6393f4ce95a9 Fri Mar 25 13:52:30 2022 -0700

• now using a bigBed file for chromAlias function refs #27228
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSendList.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text

a2c648a9f1539f12cfab4a5642b20e3550e9cd2e Fri Mar 25 13:54:35 2022 -0700

• now using a bigBed file for chromAlias function refs #27228
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 5, context: html, text, full: html, text

06c419b9e75122f425657acb9e4fbde86cce7786 Sat Mar 26 07:56:58 2022 -0700

• wait until v429 code gets out to turn on use of chromAlias.bb refs #27228
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 3, context: html, text, full: html, text

13bfd800b82e7439df8f5dce583676890139d3c4 Mon Mar 28 09:56:25 2022 -0700

• create bpt during addMask refs #28961
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 3, context: html, text, full: html, text