Commits for hiram

v395_base to v396_preview (2020-03-09 to 2020-03-16) v396

8c8cfb9ac4462733d42554c68b5338ea959569d5 Mon Mar 9 14:39:13 2020 -0700

• adding 12-way multiz no redmine
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.12way.ra - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra - lines changed 2, context: html, text, full: html, text

80b709bb9a2d2cb227dd406dd6dd7e047b410bdd Mon Mar 9 23:20:41 2020 -0700

• first pass at a multiple alignment kinda like eboVir3 needs gene frames refs #25090
  • src/hg/makeDb/doc/wuhCor1/multiz.txt - lines changed 1493, context: html, text, full: html, text

ad863edf952fc0609f53463a06e6a38d17c563b1 Mon Mar 9 23:21:53 2020 -0700

• initial view of 119-way alignment on wuhCor1 refs #25090
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 111, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

ef8d60a72021393316160d80c459dbe606ff25f3 Tue Mar 10 09:27:34 2020 -0700

• delete all the extra garbage beyond the last step performed refs #25090
  • src/hg/makeDb/doc/wuhCor1/multiz.txt - lines changed 1225, context: html, text, full: html, text

1451c6ef63b264a84ce40dc5085db67718d43a90 Tue Mar 10 14:59:55 2020 -0700

• correct species order and default off for all non SARS-CoV-2 refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 4, context: html, text, full: html, text

fdd97f11b0aaa3ce471e18e2e996bfe096645183 Wed Mar 11 09:20:44 2020 -0700

• name correspondence list refs #25090
  • src/hg/makeDb/doc/wuhCor1/nameList119.txt - lines changed 119, context: html, text, full: html, text

b378ec33475f3fd10a4cc6667cf3cbf0989f04de Wed Mar 11 10:42:50 2020 -0700

• beginning description page refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html - lines changed 527, context: html, text, full: html, text

f1a8ae4b8418c351bdc5d3ae8b8cae7dc2a90297 Wed Mar 11 15:12:58 2020 -0700

• table now has phylo distance and in that initial order refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html - lines changed 120, context: html, text, full: html, text

f08f94b43b6fb0ba32688a4121476ee2fe0618b6 Wed Mar 11 16:14:56 2020 -0700

• correct outlinks for sequences not in genbank refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html - lines changed 7, context: html, text, full: html, text

b74f05e2e998de45ee84777a2661930b3c30a2e2 Wed Mar 11 16:16:14 2020 -0700

• order by calibrated phylo distance refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 4, context: html, text, full: html, text

2981a383abe7b79b84d75f8a78ed7c83bb3938a4 Wed Mar 11 18:00:00 2020 -0700

• now with phastCons and phyloP refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 8, context: html, text, full: html, text

62ff1f5ef09a7b6ed47597de0785df40bd2c699a Thu Mar 12 13:09:55 2020 -0700

• adding epitope date from Arkal Arjun Rao extracted from https://doi.org/10.1101/2020.02.12.946087 refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

37e77c100b8953e93eb776ebd69df2685fbfcadd Thu Mar 12 13:11:44 2020 -0700

• can not use labelFields on the ncbiGene genePred track refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

18c258cd4bfc1e391c89d8fa5e4e24d54fe83054 Thu Mar 12 14:24:21 2020 -0700

• fix the NMDC*-* names to be NMCD*_* refs #25090
  • src/hg/makeDb/doc/wuhCor1/nameList119.txt - lines changed 5, context: html, text, full: html, text

00e62e8a41d36887fdbbdb7519d54a3851fdaa57 Thu Mar 12 14:35:06 2020 -0700

• phastCons and phyloP track constructions refs #25090
  • src/hg/makeDb/doc/wuhCor1/phastCons119way.txt - lines changed 358, context: html, text, full: html, text

49eae9eda65782332874d75f644479b1a5b0b51b Fri Mar 13 09:45:24 2020 -0700

• add name quoting option refs #25090
  • src/hg/utils/phyloTrees/binaryTree.pl - lines changed 12, context: html, text, full: html, text

e00236df7c5e59c822460caa58e662972af379cf Fri Mar 13 10:02:00 2020 -0700

• the quotes should be 'single' quotes refs #25090
  • src/hg/utils/phyloTrees/binaryTree.pl - lines changed 3, context: html, text, full: html, text

f29e6e6fe0b3ff481c572970b0cb777822922d14 Fri Mar 13 11:19:59 2020 -0700

• phylo tree for wuhCor1 119 way refs #25090
  • src/hg/htdocs/images/phylo/wuhCor1_119way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

2c221611ba1fe1da89314c8b9aad0bc9f5998e5c Fri Mar 13 11:28:26 2020 -0700

• add bothNames option to allow both names in output when translateName refs #25090
  • src/hg/utils/phyloTrees/binaryTree.pl - lines changed 8, context: html, text, full: html, text

77bb82402f38ead533bd99c9848a9a911d302f4b Fri Mar 13 15:42:54 2020 -0700

• phylo trees used for downloads refs #25090
  • src/hg/makeDb/doc/wuhCor1/wuhCor1.119way.descriptiveName.nh - lines changed 119, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/wuhCor1.119way.nh - lines changed 119, context: html, text, full: html, text

f7dff86f8009c87639bdc23592d9eacb16a23adb Fri Mar 13 15:43:37 2020 -0700

• done with 119 way alignment refs #25090
  • src/hg/makeDb/doc/wuhCor1/multiz.txt - lines changed 57, context: html, text, full: html, text

ff59ac0b712aadc6dc6d462cba18dbe628906cc7 Fri Mar 13 21:07:06 2020 -0700

• adding a 44-way conservation track refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

5836c9c3fbf2aaa27fdc3e9f7fb65bcc7dc7c6d2 Fri Mar 13 21:10:47 2020 -0700

• adding 44-way alignment refs #25090
  • src/hg/makeDb/doc/wuhCor1/multiz44.txt - lines changed 560, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/snpView.44way.txt - lines changed 79, context: html, text, full: html, text

b499bd792a1d81575a926a2b907fdb5f34301afd Fri Mar 13 21:11:53 2020 -0700

• slight corrections found while running up the 44 way refs #25090
  • src/hg/makeDb/doc/wuhCor1/multiz.txt - lines changed 4, context: html, text, full: html, text

7366c05d85a7b46cb465a30b9eb60730e705a5e9 Fri Mar 13 21:35:17 2020 -0700

• phastCons and phyloP calculated for 44-way refs #25090
  • src/hg/makeDb/doc/wuhCor1/phastCons44way.txt - lines changed 348, context: html, text, full: html, text

8d510f50dd31bc24f96511c16fe75142eb8585c6 Sat Mar 14 09:05:46 2020 -0700

• now have a phylo image refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 2, context: html, text, full: html, text

dfcf0922f105edcd7676f0e1cadf26ccdcb7c05c Sat Mar 14 14:07:38 2020 -0700

• image for 44-way alignment refs #25090
  • src/hg/htdocs/images/phylo/wuhCor1_44way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

9910dce6454426d225df14ccd99163c4061ab33a Sat Mar 14 14:17:56 2020 -0700

• correct viewLimits on phyloP track refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra - lines changed 3, context: html, text, full: html, text