Commits for hiram

v429_preview2 to v429_base (2022-03-28 to 2022-04-04) v429

8b71be65ac62a68201a8681bc3e7bce756011487 Mon Mar 28 12:45:39 2022 -0700

• correct symlink for chromAlias.bb refs #27228
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 2, context: html, text, full: html, text

c9f040b7cd79e62f2082a62fb0ae6ccbc90b02c6 Tue Mar 29 12:49:56 2022 -0700

• adding chainNet definition to CHM13 T2T GCA_009914755.4 assembly hub refs #28907
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 95, context: html, text, full: html, text

c371f31291a175307f0bd092439a802edee30894 Wed Mar 30 10:37:22 2022 -0700

• adding in chainNet composite for alignments to CHM13 and the two HG002 assemblies refs #28907
  • src/hg/makeDb/trackDb/human/chainNetHuman.ra - lines changed 225, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

d65e9081744ae28115fa8e5063a5d2e8938b3776 Wed Mar 30 12:06:58 2022 -0700

• reset the pull-down selection menus to look like buttons refs #28930
  • src/hg/htdocs/style/gar.css - lines changed 12, context: html, text, full: html, text

aaa182677fc86a82dd4cd7764cdb40a1476cedae Wed Mar 30 12:47:51 2022 -0700

• the selection menus now look like buttons with a down arrow icon and the column headers have an info icon refs #28930
  • src/hg/gar/garTable.pl - lines changed 19, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 2, context: html, text, full: html, text

4e9aedd9195104e098858f5908727498f3ef3e35 Wed Mar 30 15:04:15 2022 -0700

• fixup typo spelling error refs #28930
  • src/hg/gar/garTable.pl - lines changed 1, context: html, text, full: html, text

12b6db960b81f9c254ca6f864052b7ef58e20e91 Wed Mar 30 15:09:57 2022 -0700

• chainNet lastz runs to CHM13, HG002 maternal, and HG002 paternal refs #28907
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 276, context: html, text, full: html, text

74a95a0342332cbd7594d930ef1a2fa4b7ceedfb Fri Apr 1 14:12:08 2022 -0700

• procedure for crisprAll refs #29123
  • src/hg/makeDb/doc/bosTau9/initialBuild.txt - lines changed 76, context: html, text, full: html, text

addf10d08062993a60b45e52df8ddcdba57a8778 Fri Apr 1 16:46:52 2022 -0700

• documentation for the human chainNets refs #29189
  • src/hg/makeDb/trackDb/human/homoSapiensChainNet.html - lines changed 194, context: html, text, full: html, text

7fa908f40df50ecd4d078811aea7c25c5556c63a Fri Apr 1 16:47:11 2022 -0700

• documentation for the human chainNets refs #29189
  • src/hg/makeDb/trackDb/human/chainNetHuman.ra - lines changed 1, context: html, text, full: html, text

6cda00dc26e57ab505aa0c21746960e0aaa5cc73 Fri Apr 1 16:54:51 2022 -0700

• listing the genomes refs #29189
  • src/hg/makeDb/trackDb/human/homoSapiensChainNet.html - lines changed 11, context: html, text, full: html, text

9f07e62e4e0365ac134e37a9aae3442cf5fe1dc9 Fri Apr 1 16:59:09 2022 -0700

• typo error for link fixed refs #29182
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgLiftOver.html - lines changed 4, context: html, text, full: html, text

072c63e3652fb81f83a3db79363a0f841a488aae Fri Apr 1 17:13:40 2022 -0700

• type error for liftover-mask.bed reference refs #29182
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgLiftOver.html - lines changed 1, context: html, text, full: html, text