Commits for hiram

v405_preview to v405_preview2 (2020-09-21 to 2020-09-28) v405

f619ad52904568bd108d65e34d2e10cb381f439e Mon Sep 21 14:04:09 2020 -0700

• now recognizing assembly hub chromAlias file to allow bed type custom tracks with other names refs #24396
  • src/hg/lib/hdb.c - lines changed 28, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 19, context: html, text, full: html, text

c270fe6ea9ae2701f1d41dc3b4180ac511dff187 Mon Sep 21 14:55:35 2020 -0700

• initial script works only on araTha refs #24396
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 161, context: html, text, full: html, text

464d0311d4ec35f8ffe669e3ef75aa7f374ba926 Mon Sep 21 17:44:51 2020 -0700

• begin to work in the chromAlias construction to the assembly hubs refs #24396
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 120, context: html, text, full: html, text

9ca89f9ff4facb407acfd0a8e970472a45be29a0 Tue Sep 22 11:48:06 2020 -0700

• adding chrom.sizes as download file for hgTracks sequences in assembly hubs refs #24396
  • src/hg/hgTracks/hgTracks.c - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 28, context: html, text, full: html, text

ea3c06ec82f3f1df48c529c77d2667ead355edf3 Tue Sep 22 11:51:11 2020 -0700

• adding chrom.sizes as download file for hgTracks sequences in assembly hubs refs #24396
  • src/hg/inc/trackHub.h - lines changed 8, context: html, text, full: html, text

46d4388aa7f2d939c4712d33053812d7ec1a7f97 Wed Sep 23 09:55:39 2020 -0700

• accomodate duplicate sequences refs #24396
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 78, context: html, text, full: html, text

4f09e8ddd0fc70577eb8727e38a87896bfd57e84 Wed Sep 23 09:56:28 2020 -0700

• adding chromAlias build refs #24396
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 39, context: html, text, full: html, text

b1852a4dd2bbc53c29c822f0d6a0e40d1af7a713 Wed Sep 23 10:11:32 2020 -0700

• accomodate duplicate sequences refs #24396
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 2, context: html, text, full: html, text

c11977132896e151af8ce9254baa6d5b130e9b40 Fri Sep 25 11:16:33 2020 -0700

• update to new make system refs #23891
  • src/hg/makeDb/doc/primatesAsmHub/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 22, context: html, text, full: html, text

cbde4b68d111496a694ee94430b6d64511d620e7 Fri Sep 25 12:45:04 2020 -0700

• update to new make system refs #23891
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/makefile - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/makefile - lines changed 1, context: html, text, full: html, text