Commits for hiram

v387_base to v388_preview (2019-09-02 to 2019-09-09) v388

7873ad671c469a1c6c8b6d249dc4123e6d82e361 Wed Sep 4 08:35:13 2019 -0700

• lastz chainNet hg19 to rheMac10 refs #23771
  • src/hg/makeDb/doc/hg19.txt - lines changed 74, context: html, text, full: html, text

cdcf1185869b54c6ba17f3776a48f331587cbe62 Wed Sep 4 08:35:56 2019 -0700

• catching up with table contents on ce11 refs #23589
  • 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/list08.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)

a3801c8acc3bee5d65e260dcd842d615be11b3a6 Wed Sep 4 10:18:46 2019 -0700

• list schema needs to handle big* files correctly refs #23589
  • src/hg/hubApi/list.c - lines changed 62, context: html, text, full: html, text

99366c9bb1c519f7cbea16412c4b120d2c773eba Wed Sep 4 10:19:24 2019 -0700

• list schema needs to handle big* files correctly refs #23589
  • src/hg/hubApi/tests/expected/schema01.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/schema02.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/schema03.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/schema07.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

f4e9ca27e2813217552c483235a528c0dd5edd19 Wed Sep 4 10:20:47 2019 -0700

• list schema needs to handle big* files correctly refs #23589
  • src/hg/hubApi/tests/makefile - lines changed 13, context: html, text, full: html, text

b1311c5c3363277be89c7cd02a07a71193a48df8 Wed Sep 4 10:27:45 2019 -0700

• catching up with new trackDb definitions refs #23589
  • 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)

381513b45ce805dd0f5f68c3fc528e8e90dda504 Thu Sep 5 14:44:28 2019 -0700

• validate end coordinate for sequence request is within chromSize refs #24089
  • src/hg/hubApi/getData.c - lines changed 4, context: html, text, full: html, text

c69ee33290bf5f6bdc44b8c56181fd5c5aa16701 Thu Sep 5 16:22:07 2019 -0700

• also check end coordinate vs chromSize for hub genome 2bit sequence getData refs #24089
  • src/hg/hubApi/getData.c - lines changed 4, context: html, text, full: html, text

3f1d82c774cbe9e92f0b3e5dfc5323a0d17a0baf Thu Sep 5 16:27:45 2019 -0700

• also check end coordinate vs chromSize for hub genome 2bit sequence getData refs #24089
  • src/hg/hubApi/tests/expected/getSeq04.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/getSeq05.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/redmine24089a.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/redmine24089b.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/test6.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/test7.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

7c28bed1b8d3dd630b67d92a4a784eab1d56c0ea Thu Sep 5 16:34:12 2019 -0700

• also check end coordinate vs chromSize for hub genome 2bit sequence getData refs #24089
  • src/hg/hubApi/tests/makefile - lines changed 35, context: html, text, full: html, text

39cf3af89847e9fd3ecda1fdcd6453abb52f9590 Sun Sep 8 17:24:52 2019 -0700

• initial files from makeGenomeDb.pl refs #21579
  • src/hg/makeDb/trackDb/rat/regenRn1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/regenRn1/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/regenRn1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/regenRn1/trackDb.ra - lines changed 8, context: html, text, full: html, text

4fdac1a09cb6a154a2f739885b02fc8f0e40a00d Mon Sep 9 09:57:59 2019 -0700

• first instance of hub is complete refs #23734
  • src/hg/makeDb/doc/VGP/README.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/bigDensity.pl - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/hub.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkAsmStats.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkGenomes.pl - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkSymLinks.sh - lines changed 3, context: html, text, full: html, text

249b307f8e7edcaa916870d673678044c478e953 Mon Sep 9 09:59:05 2019 -0700

• Adding Ensembl alias with v95 release refs #22425
  • src/hg/makeDb/doc/bosTau9/initialBuild.txt - lines changed 15, context: html, text, full: html, text

d8751b5445ffe3667e72aeb5041b724a1877a392 Mon Sep 9 10:00:16 2019 -0700

• initial build is sufficient for Mark.s testing refs #22271
  • src/hg/makeDb/doc/GRCm38B/initialBuild.txt - lines changed 296, context: html, text, full: html, text

d13887bf1bc4a13e590d7c1ff16b2d81b2cdb18e Mon Sep 9 10:01:11 2019 -0700

• added chromAlias table no redmine
  • src/hg/makeDb/doc/pteVam1.txt - lines changed 49, context: html, text, full: html, text

f630e910fa3bf0edff8347bd8c914606318c041e Mon Sep 9 10:02:02 2019 -0700

• liftOver to rheMac10 refs #23771
  • src/hg/makeDb/doc/rheMac8/initialBuild.txt - lines changed 18, context: html, text, full: html, text