Commits for hiram

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800

• adding track descriptions from Lindblat-Toh group refs #25279
  • src/hg/makeDb/trackDb/dog/canFam4/altAllele.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam4/altAllele.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam4/miRNA.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam4/structVar.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam4/uuGene.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam4/uuGene.ra - lines changed 2, context: html, text, full: html, text

549cc338cbe2531334b345274c87fac55edee6c2 Mon Dec 7 13:01:44 2020 -0800

• adding annotations from Lindblad-Toh lab refs #26657
  • src/hg/makeDb/doc/canFam4/initialBuild.txt - lines changed 43, context: html, text, full: html, text

4249ea7c261b62acbdff737b76468640e7ffa9eb Mon Dec 7 13:18:05 2020 -0800

• adding annotations from Lindblad-Toh lab refs #26657
  • src/hg/makeDb/doc/canFam4/initialBuild.txt - lines changed 2, context: html, text, full: html, text

90720ea4153ead9a125115daa0272dba39d3927b Mon Dec 7 14:06:40 2020 -0800

• documentation how to operate this process refs #23891
  • src/hg/makeDb/doc/asmHubs/README.txt - lines changed 128, context: html, text, full: html, text

f6d8c8393632dfff192a1287ecce346cb83469d9 Tue Dec 8 11:09:16 2020 -0800

• try using bigPsl display parameters as used by blat custom track refs #24672
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 5, context: html, text, full: html, text

b9a38e782ce3445f2e73876c9664ccd125794ded Tue Dec 8 11:18:09 2020 -0800

• better genomicCodons for baseColorDefault on LRG bigPsl refs #24672
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text

6289d9f62a0feda12bb77d511003fa7c06d4a610 Tue Dec 8 13:44:32 2020 -0800

• catching up to current set including plants refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 77, context: html, text, full: html, text

6a32124d5346a77980465373a1f78692956ff721 Wed Dec 9 14:49:45 2020 -0800

• adding definition for Chinese hamster now with dots in sequence names as well as assembly/organism name refs #26584
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 57, context: html, text, full: html, text

6d3ef228a206f70d8cde9e5e89d280e7d7c6000b Thu Dec 10 14:53:57 2020 -0800

• first pass on plants hub listings refs #23891
  • src/hg/makeDb/doc/plantsAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/makefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 109, context: html, text, full: html, text

3dd09a4b5f9dd8ad5122483b7b040dcec14ac1f4 Mon Dec 14 16:40:51 2020 -0800

• lastz chainNet per user request hg19 bosTau9 refs #26638
  • src/hg/makeDb/doc/hg19.txt - lines changed 77, context: html, text, full: html, text

2aef12dde4b14b26e8bb10a5b6670ad772a4c6dc Mon Dec 14 16:41:42 2020 -0800

• catching up hubs done refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 11, context: html, text, full: html, text

8dc7ac330f07414e7225020625b651c2f135e662 Mon Dec 14 17:15:28 2020 -0800

• catching up hubs done and now matching hgdownload dir list refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 28, context: html, text, full: html, text

f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800

• catching up recently built hubs refs #23891
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 9, 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 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv - lines changed 1, context: html, text, full: html, text

e1bad6bcd71bef15344d18cd16d2e416b9840078 Mon Dec 14 19:00:35 2020 -0800

• a copy of index.html from hgdownload (generated there by script) update to today refs #23891
  • src/hg/makeDb/doc/asmHubs/hgdownload.index.html - lines changed 75, context: html, text, full: html, text

123fabea3a7c3d2877818bfe27bcfaf49bbf0c58 Mon Dec 14 22:52:47 2020 -0800

• beware blanks in sequence names refs #23891
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 3, context: html, text, full: html, text

2080e04c842d2016e324d9e31fe0a7b4e867f976 Fri Dec 18 12:39:01 2020 -0800

• viewing maf file from Cactus 241-way alignment refs #11636
  • src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

3c614c8b6f65a275dec519d292b870afeec12335 Sat Dec 19 09:07:59 2020 -0800

• multiz done running up iRows refs #26584
  • src/hg/makeDb/doc/mm39/multiz35way.txt - lines changed 2250, context: html, text, full: html, text

69e951f0f4d62bc8577211a850d73a4199e4b72a Sat Dec 19 15:57:28 2020 -0800

• mm39 35-way now with maf summary table refs #26584
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 1, context: html, text, full: html, text

fa579fd8c0dd3c21af3673f3f606a1093d141f68 Sun Dec 20 23:21:20 2020 -0800

• more correct grouping of species refs #26584
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra - lines changed 11, context: html, text, full: html, text

d709b2a9f0d7ecffd5a80066f99882a05ec334e7 Mon Dec 21 14:35:42 2020 -0800

• begin to organize into clades refs #11636
  • src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra - lines changed 8, context: html, text, full: html, text

b58decb00bc76c1cf7335f186f71875c0baca4bf Mon Dec 21 14:36:49 2020 -0800

• clades for hg38 241-way refs #11636
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 4, context: html, text, full: html, text

59afd780130dec857011bcad89e2c496d034ace6 Mon Dec 21 15:04:58 2020 -0800

• image for mm39 35-way alignment refs #26584
  • src/hg/htdocs/images/phylo/mm39_35way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

2591cf6978567ffca7f402d6311000810993d196 Mon Dec 21 15:38:40 2020 -0800

• output chain stats table for 35-way refs #26584
  • src/hg/makeDb/doc/mm39/sizeStats.pl - lines changed 111, context: html, text, full: html, text

346748ca6fae57c82810e5ae94166c7f5547b940 Mon Dec 21 15:39:19 2020 -0800

• read to continue with gene annotation refs #26584
  • src/hg/makeDb/doc/mm39/multiz35way.txt - lines changed 171, context: html, text, full: html, text

95599ae77e60f8b8a9bbfc9894e9051afbfe9384 Tue Dec 22 09:45:44 2020 -0800

• frames done refs #26584
  • src/hg/makeDb/doc/mm39/multiz35way.txt - lines changed 491, context: html, text, full: html, text

051feecd9e300cf077787a56af4cd1b9dd4fb497 Tue Dec 22 10:36:30 2020 -0800

• turing on frames refs #26584
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra - lines changed 1, context: html, text, full: html, text

2b7291b093bad5d90337189e1de7a7168f049439 Tue Dec 22 21:22:38 2020 -0800

• now with phastCons and phyloP and mostConserved refs #26584
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra - lines changed 4, context: html, text, full: html, text

c4700dd1959b6c45050fbb1b0733397d58916f57 Tue Dec 22 21:34:32 2020 -0800

• ready for downloads and running up hgPal files refs #25864
  • src/hg/makeDb/doc/mm39/multiz35way.txt - lines changed 351, context: html, text, full: html, text

9f629656dd1bb546fb3e222ae28e9c68486936cb Wed Dec 23 17:03:31 2020 -0800

• ready for wiki summary pages and download README files refs #25864
  • src/hg/makeDb/doc/mm39/multiz35way.txt - lines changed 34, context: html, text, full: html, text