Commits for hiram

v404_base to v405_preview (2020-09-14 to 2020-09-21) v405

411acf92db70f5f7a8584cb3cad643b88d4aeabc Mon Sep 14 15:04:51 2020 -0700

• additional rules for canFam5 refs #25917
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text

2986dc8f9e9b8e1d276f8dbc981309fba29d9016 Mon Sep 14 16:39:05 2020 -0700

• completed marked QA Ready refs #25917
  • src/hg/makeDb/doc/canFam5/initialBuild.txt - lines changed 193, context: html, text, full: html, text

41ac5854aee6292610b1519e69d107116c8b9e22 Wed Sep 16 08:27:15 2020 -0700

• adding NCBI and Ensembl transcript and protein IDs to the genePred output refs #24672;
  • src/hg/utils/automation/parseLrgXml.pl - lines changed 28, context: html, text, full: html, text

27e330737ba88fc3682f401974d8cab1b2fa841b Wed Sep 16 14:02:58 2020 -0700

• prototype for new style LRG Fixed Transcript Annotations refs #24672
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 26, context: html, text, full: html, text

5736c27ba84cabf7298c075d3eb915de415cb2a7 Wed Sep 16 14:05:37 2020 -0700

• prototype for new style LRG Fixed Transcript Annotations refs #24672
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 3, context: html, text, full: html, text

17748af09f0add98009e2c4c181cb4e75d068d26 Wed Sep 16 14:17:15 2020 -0700

• modified procedure to make a new style LRG transcript track refs #24672
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 28, context: html, text, full: html, text

531083fac3b99f775f940e7b124c88a0d41fc386 Thu Sep 17 11:20:04 2020 -0700

• recover function of local lift file when on db assembly refs #24074
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 4, context: html, text, full: html, text

02b770de07c1c9f575406b32ea3ce241fbefaeb1 Thu Sep 17 11:21:35 2020 -0700

• now with NCBI RefSeq track refs #24074
  • src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra - lines changed 2, context: html, text, full: html, text

180734e3da31c25fecc1583231a29885abc1d18b Thu Sep 17 12:00:59 2020 -0700

• pretty close to done refs #24074
  • src/hg/makeDb/doc/calJac4/initialBuild.txt - lines changed 224, context: html, text, full: html, text

cd3cb167196e74d31050cd822634a4529a1ebf01 Thu Sep 17 18:09:51 2020 -0700

• show chrom alias names on sequence display page refs #24396
  • src/hg/hgTracks/hgTracks.c - lines changed 59, context: html, text, full: html, text

cb8f8b8e1fa7a5e122b4e0e5c7fb84bf4027d008 Fri Sep 18 13:03:08 2020 -0700

• assembly hubs and now display alias names on sequence display page refs #24396
  • src/hg/hgTracks/hgTracks.c - lines changed 30, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 116, context: html, text, full: html, text

baca98f3366561495cb20ac6ecb41c8794daf34d Fri Sep 18 14:27:22 2020 -0700

• fix last row of table to correctly have three columns when required refs #24396
  • src/hg/hgTracks/hgTracks.c - lines changed 36, context: html, text, full: html, text