Commits for hiram

v444_preview to v444_preview2 (2023-02-06 to 2023-02-13) v444

f8c99a35bd085c9ec73b730a382129fee2183570 Mon Feb 6 14:47:27 2023 -0800

• add in the repeatModeler download files no redmine
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 10, context: html, text, full: html, text

8c39e9cdaef1aae3e50691b4452a118a8ddb4fd8 Mon Feb 6 14:48:14 2023 -0800

• error out when clade definition is missing no redmine
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 5, context: html, text, full: html, text

129709f4ebba14b4ed271d9ee0c71b250e38294d Mon Feb 6 15:04:25 2023 -0800

• adding GCF_900747795.2_fErpCal1.3 reedfish/Erpetoichthys_calabaricus to catch up for VGP no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

631b1158bd10f31933723570979fa8aec1de321d Mon Feb 6 15:26:37 2023 -0800

• updated assembly for reedfish GCF_900747795.1_fErpCal1.1 no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

64d447ba2e30d43e88dfdf32ee98ff045888ee60 Mon Feb 6 15:39:50 2023 -0800

• GCA_004115265.2 replaced by GCF_004115265.2 no redmine;
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 1, context: html, text, full: html, text

8f64dc6018ec35583b8f807758e0fb12d8d45e9c Tue Feb 7 11:56:45 2023 -0800

• updated expected test output to reflect today contents of tables on hgwdev no redmine
  • src/hg/hubApi/tests/expected/list03.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list09.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/test0.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/test41.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

e7071512b2fa2f30e99a5b47f32f30cbda67a4fe Tue Feb 7 12:02:48 2023 -0800

• updated expected test output to reflect today contents of tables on hgwdev no redmine
  • src/hg/hubApi/tests/expected/schema06.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/schema10.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

4a3f103195afff216604e84a30fc1d1ed4e0cf82 Tue Feb 7 12:13:35 2023 -0800

• indicate comments which server is which CGI no redmine
  • src/hg/hubApi/tests/jsonConsumer.pl - lines changed 3, context: html, text, full: html, text

a9667a778e3a95abce27ccc2b0c8d84f4bf3da8a Tue Feb 7 12:45:04 2023 -0800

• trackDb updates affect the results of tests, make sure up to date no redmine
  • src/hg/hubApi/tests/expected/list03.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list09.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/schema06.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/schema10.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/test41.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

a0e18d1f64aa38a4d79895ddf426838ec139637a Tue Feb 7 12:58:57 2023 -0800

• use a local vcfTabix track to test not supported no redmine
  • src/hg/hubApi/tests/expected/notSup02.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

1744d98b15270fdbeb3abf81ee065ddfbd20f884 Tue Feb 7 12:59:12 2023 -0800

• use a local vcfTabix track to test not supported no redmine
  • src/hg/hubApi/tests/makefile - lines changed 2, context: html, text, full: html, text

91c4d455cc5c40ca17b08695bcb9ed887c8374f7 Wed Feb 8 10:15:35 2023 -0800

• adding GCA_902829235.1_CLODIP2 mayflies C.dipterum (2020) per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

a34d583ea0c3e75e865ed31d8f32133c8f945383 Wed Feb 8 11:00:22 2023 -0800

• catch up for some missed completed builds no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

7651f710438202bebb335bd06d5a5809f254ddd2 Wed Feb 8 16:52:08 2023 -0800

• adding four new VGP assemblies to catch up no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 4, context: html, text, full: html, text

6a173139cd987a0438b9798b902e0f4ba5006062 Thu Feb 9 14:23:02 2023 -0800

• adding chainNet definitions for GCF_024166365.1 GCF_018350175.1 GCF_004115215.2 per user request refs #30555
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 206, context: html, text, full: html, text

253725f97da38e647a3f7ac58043a0022b1c4847 Thu Feb 9 15:00:07 2023 -0800

• bring in Asiatic elephant, domestic cat, and platypus GenArk hub chain tracks into composite refs #30555
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 25, context: html, text, full: html, text

e71cff44c70dc01dda7236b4d6696320c4e0e379 Fri Feb 10 08:20:38 2023 -0800

• adding two per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

267f04e1dd82e71c871c9dfb465e2d3b1aa5617e Fri Feb 10 09:53:48 2023 -0800

• add a bit more output in the failing case to help identify it and update GRCh38 to patch 14 no redmine
  • src/hg/utils/otto/grcIncident/runUpdate.sh - lines changed 8, context: html, text, full: html, text

4418dae2476e397d9c03c1301e573e2c45b1a58e Fri Feb 10 12:16:43 2023 -0800

• adding asmEquivalent functions to this library no redmine
  • src/hg/inc/asmEquivalent.h - lines changed 103, context: html, text, full: html, text
  • src/hg/lib/asmEquivalent.c - lines changed 53, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 2, context: html, text, full: html, text

cf9bdd51cff9f2d4c01f8041e4c0c4708887571b Fri Feb 10 12:18:15 2023 -0800

• moved asmEquivalent.h to ../inc where it belongs no redmine
  • src/hg/lib/asmEquivalent.h - lines changed 101, context: html, text, full: html, text

67a193695c84dcb0508c79bdc7f8549471e9c5a7 Fri Feb 10 12:50:06 2023 -0800

• using the asmEquivalent hgFixed table to get an assembly name for the GDV browser will also need to translate the chromsome name to get this to work no redmine
  • src/hg/lib/hdb.c - lines changed 5, context: html, text, full: html, text