Commits for hiram

v392_preview2 to v392_base (2019-12-16 to 2020-01-06) v392

54c4f85da2fcff075df03bbce841043e0d5acc28 Tue Dec 17 08:31:41 2019 -0800

• lastz chainNet run regenCho1 vs. rn6 refs #24568
  • src/hg/makeDb/doc/rn6.txt - lines changed 74, context: html, text, full: html, text

487174a2ad313bc229c6733ce263fb6a4413d50f Wed Dec 18 14:26:41 2019 -0800

• start=end=0 does not work for NIB fetch sequence refs #24666
  • src/hg/hubApi/getData.c - lines changed 2, context: html, text, full: html, text

bbb2c537ecb4b7736ccd5b4d038e3158ba71e382 Thu Dec 19 13:57:22 2019 -0800

• regenCho1 7-way phylo tree refs #24568
  • src/hg/htdocs/images/phylo/regenCho1_7way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800

• 7-way multiz alignment refs #24524
  • src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html - lines changed 437, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.7way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.ra - lines changed 2, context: html, text, full: html, text

9aa6bd8e92fd50cea40a4ac676493c9047ee03cd Fri Dec 20 13:15:54 2019 -0800

• documentation page for 7-way refs #21579
  • src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html - lines changed 437, context: html, text, full: html, text

dc4b56b6156979617a0a79a99746f63c0090dcd2 Fri Dec 20 13:42:30 2019 -0800

• descriptions for AGP and gap definitions from the Regeneron AGP file refs #24524
  • src/hg/makeDb/trackDb/criGri/regenCho1/regenAGP.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/regenCho1/regenAGPGap.html - lines changed 8, context: html, text, full: html, text

12b4622b8e00524ac3a6acd375fbf9a408ff41a6 Mon Dec 23 10:39:46 2019 -0800

• symlinks should be relative, not absolute refs #24354
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 31, context: html, text, full: html, text

cb83116ca0be25e3e45c93468d951fe53cb2c1e4 Fri Dec 27 00:49:20 2019 -0800

• better partitioning of the target genome refs #24354
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 26, context: html, text, full: html, text

4ca6162650c6e0f213cf674642b7a2b6bcea9bc1 Fri Dec 27 00:50:12 2019 -0800

• now automatically eliminating duplicate sequences refs #24354
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 29, context: html, text, full: html, text

e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800

• update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
  • src/hg/hubApi/apiUtils.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hubApi/tests/expected/err45.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/err47.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/redmine24666.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/makefile - lines changed 17, context: html, text, full: html, text

a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800

• fixup tests to eliminate differences between hgwdev test vs. RR site same test 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/makefile - lines changed 4, context: html, text, full: html, text

147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800

• set of files for hub build refs @24354
  • src/hg/makeDb/doc/globalReference/README.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/accAsmId.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/commonNameOrder.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/commonNames.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/ethnicGroup.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/family.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/groups.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/human.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/isolate.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/mkAsmStats.pl - lines changed 270, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/mkGenomes.pl - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/mkHubIndex.pl - lines changed 254, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/mkSymLinks.sh - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/perlPara.pl - lines changed 128, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/run10.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/runOne.sh - lines changed 153, context: html, text, full: html, text

27228c7e494674469a64cdeb61d7c4e433102f24 Thu Jan 2 13:16:14 2020 -0800

• updated text to global reference wording refs #24534
  • src/hg/makeDb/doc/globalReference/mkAsmStats.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/globalReference/mkHubIndex.pl - lines changed 9, context: html, text, full: html, text

8bde61c3efd8828518d70bfc287c600b86683f68 Thu Jan 2 13:22:14 2020 -0800

• add hub.txt and groups.txt copies refs #24354
  • src/hg/makeDb/doc/globalReference/makefile - lines changed 9, context: html, text, full: html, text

2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800

• initial set of files to create symlinks and index pages refs #20137
  • src/hg/makeDb/doc/primateAsmHub/groups.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/makefile - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/mkAsmStats.pl - lines changed 258, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl - lines changed 127, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl - lines changed 237, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/mkList.sh - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/mkSymLinks.pl - lines changed 172, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/primates.asmId.commonName.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/primateAsmHub/primates.commonName.asmId.orderList.tsv - lines changed 23, context: html, text, full: html, text

d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800

• get the gateway page a bit more generic with argument to specify refs #20137
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 1, context: html, text, full: html, text