Commits for hiram

v396_preview to v396_preview2 (2020-03-16 to 2020-03-23) v396

7502a793d1219ff6be9741878055eb873d565d9e Mon Mar 16 10:20:33 2020 -0700

• correct track type bigBed 9 + not bigBed 9+ refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

e0474e610833d8e58cc5c828b9bc99bc0e536444 Mon Mar 16 15:18:50 2020 -0700

• add 44-way description page refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html - lines changed 443, context: html, text, full: html, text

df0cd0f673fc986780f2ce78ae2b32803720f79b Mon Mar 16 15:22:01 2020 -0700

• small corrections to text refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html - lines changed 1, context: html, text, full: html, text

d7a0a8fc6582a80932f8ac14edfaefc988d08963 Tue Mar 17 09:24:16 2020 -0700

• defaultPosition reset to whole sequence refs #24851
  • src/hg/makeDb/doc/wuhCor1/initialBuild.txt - lines changed 5, context: html, text, full: html, text

92565d0dde74969729cf021838a55e94fe3147ba Wed Mar 18 09:10:10 2020 -0700

• adding the 44-way with strain names refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra - lines changed 105, context: html, text, full: html, text

449553d2b9dbbe845fb8c5fc2fca9bf016297650 Wed Mar 18 09:14:35 2020 -0700

• using html for cons44way refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra - lines changed 1, context: html, text, full: html, text

b8d4a65b4dd1c477971a7d8f6c97ef8a6bc71e2d Wed Mar 18 09:21:51 2020 -0700

• updated short and long labels from Max update refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra - lines changed 11, context: html, text, full: html, text

879041dca6623320be63dbcbfceaf82dec2bd49a Wed Mar 18 09:24:41 2020 -0700

• update default visibility refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra - lines changed 1, context: html, text, full: html, text

f20d7975d0373acb690ba6df158ed9a39786f9a1 Wed Mar 18 11:44:06 2020 -0700

• finished with 44-way track refs #25187
  • src/hg/makeDb/doc/wuhCor1/multiz44.txt - lines changed 122, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/phastCons44way.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/snpView.44way.txt - lines changed 11, context: html, text, full: html, text

1a0f4d5f930cae12004cec43fbb0cc6f34774651 Wed Mar 18 16:23:38 2020 -0700

• 12-way alignment on danRer10 per researcher request to redmine
  • src/hg/makeDb/doc/danRer10/multiz12way.txt - lines changed 1547, context: html, text, full: html, text

6091558bab452de0ba020f3e08a9d20ef9aa3d81 Wed Mar 18 19:09:58 2020 -0700

• lastz runs for 12-way alignment on danRer10 per research request no redmine
  • src/hg/makeDb/doc/danRer10/lastzRuns.txt - lines changed 222, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal6/lastzRuns.txt - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro9/lastzRuns.txt - lines changed 67, context: html, text, full: html, text

caa7d37fe23e92494b9c694c2e91c8d98e3a846c Thu Mar 19 12:51:40 2020 -0700

• document the procedure refs #24547
  • src/hg/makeDb/doc/assemblyEquivalence/README.txt - lines changed 147, context: html, text, full: html, text

b05f926380653f4581aabe1521ff12799f244925 Thu Mar 19 14:22:56 2020 -0700

• fix dates on DONE statements refs #25187
  • src/hg/makeDb/doc/wuhCor1/phastCons119way.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/phastCons44way.txt - lines changed 4, context: html, text, full: html, text

bac632e3041cdfd281733475e9429cb283266e6c Fri Mar 20 08:19:19 2020 -0700

• adding tablesIgnored for wuhCor1 refs #25187
  • src/hg/makeDb/schema/all.joiner - lines changed 15, context: html, text, full: html, text

7f4217b12c9e6a7185a37ebc4d43c40cab29b85c Fri Mar 20 13:41:16 2020 -0700

• errro out when all files can not be found refs #24547
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 1, context: html, text, full: html, text

84de43168bbf2952470fb8757c79a585c8668a8a Fri Mar 20 14:28:31 2020 -0700

• useful script to run a list of commands in a fashion similar to a parasol batch refs #24547
  • src/hg/utils/automation/perlPara.pl - lines changed 196, context: html, text, full: html, text